Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 177 of 410
Found at i:54260245 original size:29 final size:29
Alignment explanation
Indices: 54260187--54260288 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
54260177 TACCTATATC
* **
54260187 TGGCCCATTAAGCCC-AATCGTAT-TCATA
1 TGGCCCATTAGGCCCAAATCACATGT-ATA
*
54260215 TGGCCCATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
* *
54260244 TGGCCCATTAGGCCCAAATCACATTTACA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
54260273 TGGCCCATTCGGCCCA
1 TGGCCCATTAGGCCCA
54260289 GTCACATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.22
29 49 0.77
30 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATGTATA
Found at i:54260288 original size:58 final size:57
Alignment explanation
Indices: 54260178--54260288 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 57
54260168 AAATTCACAT
* ** *
54260178 ACCTATATCTGGCCCATTAAGCCCAATCGTATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAATCACATTCACATGGCCCATTAGGCCCAAATC
* * * *
54260235 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTACATGGCCCATTCGGCCCA
1 ACCTATATATGGCCCATTAAGCCC-AATCACATTCACATGGCCCATTAGGCCCA
54260289 GTCACATTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 21 0.47
58 24 0.53
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAATCACATTCACATGGCCCATTAGGCCCAAATC
Found at i:54262111 original size:14 final size:14
Alignment explanation
Indices: 54262067--54262111 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
54262057 GTACGAATGG
*
54262067 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
54262081 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54262095 AATGGTATGAACAA
1 AATGGTAGGAACAA
54262109 AAT
1 AAT
54262112 TGGTCGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.29, T:0.16
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54262620 original size:14 final size:14
Alignment explanation
Indices: 54262601--54262645 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
54262591 AAACCGACCA
*
54262601 ATTTTGTTCATACC
1 ATTTTGTTCCTACC
54262615 ATTTTGTTCCTACC
1 ATTTTGTTCCTACC
* *
54262629 CTTTCGTTCCTACC
1 ATTTTGTTCCTACC
54262643 ATT
1 ATT
54262646 CCATTCGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.49
Consensus pattern (14 bp):
ATTTTGTTCCTACC
Found at i:54263030 original size:11 final size:11
Alignment explanation
Indices: 54263014--54263063 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
54263004 TATACAAGTT
54263014 AAAAAAATCAA
1 AAAAAAATCAA
*
54263025 AAAAAAATTC-G
1 AAAAAAA-TCAA
54263036 AAAAAAATCAA
1 AAAAAAATCAA
54263047 AAAAAAAT-AA
1 AAAAAAATCAA
54263057 AAAAAAA
1 AAAAAAA
54263064 GAGTGATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.31
11 22 0.63
12 2 0.06
ACGTcount: A:0.82, C:0.06, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:54263314 original size:16 final size:17
Alignment explanation
Indices: 54263289--54263323 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
54263279 AAATTACGAG
*
54263289 AAAAGTCAAGAGAG-GT
1 AAAAGGCAAGAGAGCGT
54263305 AAAAGGCAAGAGAGCGT
1 AAAAGGCAAGAGAGCGT
54263322 AA
1 AA
54263324 GCGCATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.09, G:0.31, T:0.09
Consensus pattern (17 bp):
AAAAGGCAAGAGAGCGT
Found at i:54268300 original size:19 final size:19
Alignment explanation
Indices: 54268276--54268315 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54268266 AGCTCCCATG
54268276 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
54268295 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
54268314 TA
1 TA
54268316 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54268579 original size:25 final size:25
Alignment explanation
Indices: 54268551--54268610 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
54268541 TTGATATTTG
54268551 TGTTCACATTAGTTTGAATTAATTA
1 TGTTCACATTAGTTTGAATTAATTA
54268576 TGTTCACATTAGTTTGAATTAATTA
1 TGTTCACATTAGTTTGAATTAATTA
54268601 TGTTCACATT
1 TGTTCACATT
54268611 TCTTGCAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (25 bp):
TGTTCACATTAGTTTGAATTAATTA
Found at i:54269600 original size:14 final size:14
Alignment explanation
Indices: 54269578--54269625 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54269568 ACCTAAACCG
* *
54269578 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
54269592 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
54269606 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
54269620 ACCATT
1 ACCATT
54269626 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:54269866 original size:15 final size:15
Alignment explanation
Indices: 54269846--54269893 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54269836 TCAAAGATGG
54269846 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
54269861 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
54269875 GTTTATGGATATAAA
1 GTTTATGGATATGAA
54269890 GTTT
1 GTTT
54269894 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:54269880 original size:14 final size:14
Alignment explanation
Indices: 54269840--54269883 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54269830 AAGGATTCAA
54269840 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
54269854 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
54269869 AGATGGGTTTATGG
1 AGATGGGTTTATGG
54269883 A
1 A
54269884 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:54269909 original size:29 final size:29
Alignment explanation
Indices: 54269840--54269899 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54269830 AAGGATTCAA
*
54269840 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
54269869 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
54269898 AG
1 AG
54269900 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:54273312 original size:12 final size:12
Alignment explanation
Indices: 54273279--54273312 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54273269 TGTTCTTTTT
*
54273279 CTTTTTCAACGA
1 CTTTTTCAATGA
54273291 CTTTTTCAATGA
1 CTTTTTCAATGA
*
54273303 CTTTCTCAAT
1 CTTTTTCAAT
54273313 CTCTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:54274265 original size:11 final size:12
Alignment explanation
Indices: 54274249--54274277 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54274239 TTGTTTGAAA
54274249 TTTTTTTCGTTT
1 TTTTTTTCGTTT
54274261 TTTTTTTCGTTT
1 TTTTTTTCGTTT
54274273 TTTTT
1 TTTTT
54274278 GAAACTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTTCGTTT
Found at i:54274518 original size:15 final size:15
Alignment explanation
Indices: 54274498--54274545 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54274488 TCAAAGATGG
54274498 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
54274513 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
54274527 GTTTATGGATATAAA
1 GTTTATGGATATGAA
54274542 GTTT
1 GTTT
54274546 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:54274532 original size:14 final size:14
Alignment explanation
Indices: 54274492--54274535 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54274482 AAGGATTCAA
54274492 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
54274506 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
54274521 AGATGGGTTTATGG
1 AGATGGGTTTATGG
54274535 A
1 A
54274536 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:54274561 original size:29 final size:29
Alignment explanation
Indices: 54274492--54274551 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54274482 AAGGATTCAA
*
54274492 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
54274521 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
54274550 AG
1 AG
54274552 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:54278119 original size:8 final size:8
Alignment explanation
Indices: 54278102--54278136 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
54278092 GTAGCCAAAC
54278102 TTTTGGCA
1 TTTTGGCA
*
54278110 TTTTGACA
1 TTTTGGCA
*
54278118 TTTCGGCA
1 TTTTGGCA
54278126 TTTTGGCA
1 TTTTGGCA
54278134 TTT
1 TTT
54278137 CGGCTTTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.51
Consensus pattern (8 bp):
TTTTGGCA
Found at i:54278127 original size:16 final size:16
Alignment explanation
Indices: 54278106--54278144 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54278096 CCAAACTTTT
54278106 GGCATTTTGACATTTC
1 GGCATTTTGACATTTC
*
54278122 GGCATTTTGGCATTTC
1 GGCATTTTGACATTTC
54278138 GGC-TTTT
1 GGCATTTT
54278145 ACCGGTTCAT
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:0.13, C:0.18, G:0.23, T:0.46
Consensus pattern (16 bp):
GGCATTTTGACATTTC
Found at i:54280244 original size:11 final size:11
Alignment explanation
Indices: 54280230--54280259 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54280220 AAATAACAGC
54280230 AAAACAATAAG
1 AAAACAATAAG
*
54280241 AAAACAACAAG
1 AAAACAATAAG
54280252 AAAACAAT
1 AAAACAAT
54280260 CCAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.73, C:0.13, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAACAATAAG
Found at i:54299351 original size:27 final size:25
Alignment explanation
Indices: 54299307--54299511 Score: 124
Period size: 27 Copynumber: 7.6 Consensus size: 25
54299297 TTAGTTTACC
*
54299307 AAATTACTGAAATACCCCCAGTTGTA
1 AAATTAC-CAAATACCCCCAGTTGTA
* *
54299333 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAA-TACCCCCAG-TTGTA
* * *
54299360 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTA-CCAAATA-CCCCCAGTTGTA
* *
54299387 AAATTATCAAAATACCCTCAGTTTGTA
1 AAATTA-CCAAATACCCCCAG-TTGTA
* * *
54299414 AAATTACTGAAATACCCTC-GATTAATA
1 AAATTAC-CAAATACCCCCAG-TT-GTA
**
54299441 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACC-AAATACCCCCAG-TTGTA
* * *
54299468 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACC-AAATACCCC-CAGTTGTA
54299495 AAATTACCGAAATACCC
1 AAATTACC-AAATACCC
54299512 TTGTAGGGTA
Statistics
Matches: 142, Mismatches: 27, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.02
26 22 0.15
27 106 0.75
28 11 0.08
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (25 bp):
AAATTACCAAATACCCCCAGTTGTA
Found at i:54299416 original size:54 final size:53
Alignment explanation
Indices: 54299328--54299512 Score: 201
Period size: 54 Copynumber: 3.4 Consensus size: 53
54299318 ATACCCCCAG
* * * *
54299328 TTGTAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATA-CCTCGAT
* * **
54299382 TTGTAAAATTATCAAAATACCCTCAGTTTGTAAAATTACTGAAATACCCTCGAT
1 TTGTAAAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATA-CCTCGAT
** * *
54299436 TAATAAAATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACCAAAATACCCTC-GGTTTGTAAAATTACCAAAATACCTC-GAT
* *
54299490 TTGTGAAATTACCGAAATACCCT
1 TTGTAAAATTACCAAAATACCCT
54299513 TGTAGGGTAG
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
53 4 0.04
54 104 0.96
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (53 bp):
TTGTAAAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATACCTCGAT
Found at i:54299442 original size:81 final size:79
Alignment explanation
Indices: 54299307--54299512 Score: 227
Period size: 81 Copynumber: 2.5 Consensus size: 79
54299297 TTAGTTTACC
** * * * * *
54299307 AAATTACTGAAATACCCCCAG-TTGTAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCCAA
1 AAATTACCAAAATA-CCCCAGTTTGTAAAATTACGAAA-TACCCTCGATTAATAAAATTACCAAA
*
54299371 ATA-TCCTCGATTTGTA
64 ATACCCCT-GATTTGTA
*
54299387 AAATTATCAAAATACCCTCAGTTTGTAAAATTACTGAAATACCCTCGATTAATAAAATTACCAAA
1 AAATTACCAAAATACCC-CAGTTTGTAAAATTAC-GAAATACCCTCGATTAATAAAATTACCAAA
*
54299452 ATACCCCTGGTTTGTA
64 ATACCCCTGATTTGTA
* *
54299468 AAATTACCAAAATACCCCTAATTTGTGAAATTACCGAAATACCCT
1 AAATTACCAAAATACCCC-AGTTTGTAAAATTA-CGAAATACCCT
54299513 TGTAGGGTAG
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
79 3 0.03
80 15 0.14
81 82 0.77
82 7 0.07
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (79 bp):
AAATTACCAAAATACCCCAGTTTGTAAAATTACGAAATACCCTCGATTAATAAAATTACCAAAAT
ACCCCTGATTTGTA
Found at i:54299526 original size:27 final size:27
Alignment explanation
Indices: 54299496--54299699 Score: 327
Period size: 27 Copynumber: 7.6 Consensus size: 27
54299486 TAATTTGTGA
*
54299496 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299523 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
54299550 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299577 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299604 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299631 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299658 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54299685 AATTACCGAGATACC
1 AATTACCGAAATACC
54299700 TTGTGGGATA
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 164 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54300158 original size:25 final size:25
Alignment explanation
Indices: 54300122--54300215 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
54300112 CATTCACATT
54300122 CTGATT-TGATTTTG-TTACCTGATA-
1 CTGATTCTGATTTTGATT--CTGATAC
*
54300146 CTGATTCTGATTTTGATTCTGTTAC
1 CTGATTCTGATTTTGATTCTGATAC
*
54300171 CTGATACTGATTTTGATTCTG-TCAC
1 CTGATTCTGATTTTGATTCTGAT-AC
* * *
54300196 CTAATTCTAATTCTGATTCT
1 CTGATTCTGATTTTGATTCT
54300216 AGTTCTGATA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.20
25 46 0.77
26 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (25 bp):
CTGATTCTGATTTTGATTCTGATAC
Found at i:54300169 original size:31 final size:31
Alignment explanation
Indices: 54300119--54300188 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
54300109 TTGCATTCAC
*
54300119 ATTCTGA-TTTGATTTTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
54300149 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
54300180 ATTTTGATT
1 ATTCTGATT
54300189 CTGTCACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 7 0.19
31 30 0.81
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:54300212 original size:31 final size:29
Alignment explanation
Indices: 54300119--54300213 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 29
54300109 TTGCATTCAC
*
54300119 ATTCTGA-TTTGATTTTGTTACCTGATACT
1 ATTCTGATTTTGATTCTGTTACCTGAT-CT
54300148 GATTCTGATTTTGATTCTGTTACCTGA--T
1 -ATTCTGATTTTGATTCTGTTACCTGATCT
* *
54300176 A--CTGATTTTGATTCTGTCACCTAATTCT
1 ATTCTGATTTTGATTCTGTTACCTGA-TCT
54300204 AATTCTGATT
1 -ATTCTGATT
54300214 CTAGTTCTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
25 21 0.38
27 1 0.02
28 2 0.04
29 1 0.02
30 7 0.13
31 23 0.42
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTCTGATTTTGATTCTGTTACCTGATCT
Found at i:54303504 original size:14 final size:14
Alignment explanation
Indices: 54303467--54303503 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
54303457 ATACAAGTTT
54303467 GAAAAAAAAATTCC
1 GAAAAAAAAATTCC
54303481 GAAAAAAAAATT-C
1 GAAAAAAAAATTCC
54303494 GAAAAAAAAA
1 GAAAAAAAAA
54303504 AAGTGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.73, C:0.08, G:0.08, T:0.11
Consensus pattern (14 bp):
GAAAAAAAAATTCC
Found at i:54317375 original size:30 final size:30
Alignment explanation
Indices: 54317341--54317424 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
54317331 TAAACTAAAA
* *
54317341 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
54317371 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
54317401 TGAGC-AAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
54317425 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:54319402 original size:30 final size:30
Alignment explanation
Indices: 54319368--54319464 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54319358 TAAACTAAAA
54319368 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54319398 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54319428 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54319458 TGAGCTA
1 TGAGCTA
54319465 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54319756 original size:32 final size:32
Alignment explanation
Indices: 54319715--54319812 Score: 196
Period size: 32 Copynumber: 3.1 Consensus size: 32
54319705 TATGGAGTAC
54319715 TTTATCGATTATTTCGGATAGGGATCTCAAAT
1 TTTATCGATTATTTCGGATAGGGATCTCAAAT
54319747 TTTATCGATTATTTCGGATAGGGATCTCAAAT
1 TTTATCGATTATTTCGGATAGGGATCTCAAAT
54319779 TTTATCGATTATTTCGGATAGGGATCTCAAAT
1 TTTATCGATTATTTCGGATAGGGATCTCAAAT
54319811 TT
1 TT
54319813 ACTTCGCATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (32 bp):
TTTATCGATTATTTCGGATAGGGATCTCAAAT
Found at i:54329591 original size:17 final size:17
Alignment explanation
Indices: 54329550--54329592 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
54329540 TGCACTTAAG
54329550 CCATTCATGCATTCTAT
1 CCATTCATGCATTCTAT
54329567 -CATCTCATGCATT-TGAT
1 CCAT-TCATGCATTCT-AT
54329584 CCATTCATG
1 CCATTCATG
54329593 GACCAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (17 bp):
CCATTCATGCATTCTAT
Found at i:54330023 original size:30 final size:30
Alignment explanation
Indices: 54329989--54330085 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
54329979 TAAACTAAAA
*
54329989 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54330019 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54330049 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54330079 TGAGCTA
1 TGAGCTA
54330086 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54332260 original size:30 final size:30
Alignment explanation
Indices: 54332189--54332271 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 30
54332179 CTTTTGTTTC
*
54332189 AATTTCTTTTTCATATTCTTTTTCACTCTCA
1 AATTTCTTTTTCAT-TTCTTTTTCAATCTCA
*
54332220 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATT-TCTTTTTCAATCTCA
*
54332249 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTCA-TTTCTTTTT
54332272 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 6 0.13
30 31 0.69
31 8 0.18
ACGTcount: A:0.14, C:0.20, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCATTTCTTTTTCAATCTCA
Found at i:54332271 original size:18 final size:18
Alignment explanation
Indices: 54332222--54332277 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54332212 CACTCTCAAA
* *
54332222 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
54332239 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
54332257 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
54332276 TT
1 TT
54332278 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:54332278 original size:12 final size:12
Alignment explanation
Indices: 54332247--54332271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54332237 TTTTTCAATC
54332247 TCATTTTCTTTT
1 TCATTTTCTTTT
54332259 TCATTTTCTTTT
1 TCATTTTCTTTT
54332271 T
1 T
54332272 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54332350 original size:5 final size:5
Alignment explanation
Indices: 54332340--54332396 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54332330 CTCTTGCCTC
*
54332340 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
54332387 TCTTT TCTTT
1 TCTTT TCTTT
54332397 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:54332360 original size:15 final size:14
Alignment explanation
Indices: 54332340--54332403 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
54332330 CTCTTGCCTC
54332340 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
54332355 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
54332370 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
*
54332387 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
54332401 TCT
1 TCT
54332404 CTTTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.24
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:54332372 original size:25 final size:25
Alignment explanation
Indices: 54332344--54332392 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
54332334 TGCCTCTCTT
54332344 TTCTTTT-TATTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTCTTTTTC
*
54332369 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTATTTCTTTTCTTTT
54332393 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTATTTCTTTTCTTTTTC
Found at i:54332397 original size:21 final size:21
Alignment explanation
Indices: 54332340--54332407 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
54332330 CTCTTGCCTC
*
54332340 TCTTTTCTTTT-TATTTCTTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
54332361 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
54332382 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
54332402 CTCTTT
1 -TCTTT
54332408 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 7 0.17
21 28 0.70
22 5 0.12
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:54333072 original size:30 final size:31
Alignment explanation
Indices: 54333038--54333134 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54333028 AGCTCACTAC
*
54333038 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54333068 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54333098 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54333128 TAGCTCA
1 TAGCTCA
54333135 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54334692 original size:30 final size:30
Alignment explanation
Indices: 54334658--54334755 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
54334648 AGCTCACTCC
54334658 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
54334688 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
54334718 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
54334748 TAGCTCAT
1 TAGCTCAT
54334756 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:54336748 original size:12 final size:12
Alignment explanation
Indices: 54336732--54336790 Score: 88
Period size: 11 Copynumber: 5.2 Consensus size: 12
54336722 ATTAAACACT
*
54336732 TTTTTTTTAG-A
1 TTTTTTTTCGAA
54336743 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54336755 TTTTTTTT-GAA
1 TTTTTTTTCGAA
54336766 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54336778 TTTTTTTT-GAA
1 TTTTTTTTCGAA
54336789 TT
1 TT
54336791 GTATAACTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
11 25 0.56
12 20 0.44
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54336762 original size:23 final size:23
Alignment explanation
Indices: 54336731--54336790 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
54336721 CATTAAACAC
*
54336731 TTTTTTTTTAGATTTTTTTTCGAA
1 TTTTTTTTGA-ATTTTTTTTCGAA
54336755 TTTTTTTTGAATTTTTTTTCGAA
1 TTTTTTTTGAATTTTTTTTCGAA
54336778 TTTTTTTTGAATT
1 TTTTTTTTGAATT
54336791 GTATAACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 26 0.74
24 9 0.26
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (23 bp):
TTTTTTTTGAATTTTTTTTCGAA
Found at i:54338022 original size:14 final size:14
Alignment explanation
Indices: 54338003--54338047 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
54337993 AACTCATCTT
*
54338003 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
54338017 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
54338030 AATTTAATTTAATG
1 AGTTTAATTTAATG
54338044 AGTT
1 AGTT
54338048 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:54339056 original size:29 final size:29
Alignment explanation
Indices: 54339023--54339082 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54339013 ATAACCAAAC
*
54339023 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
54339052 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
54339081 CT
1 CT
54339083 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:54339075 original size:15 final size:15
Alignment explanation
Indices: 54339029--54339076 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54339019 AAACCTACAA
*
54339029 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
54339044 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
54339058 AAACTTCATATCCAT
1 AAACTTCATATCCAT
54339073 AAAC
1 AAAC
54339077 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:54345333 original size:21 final size:22
Alignment explanation
Indices: 54345307--54345350 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
54345297 GAAACAGCTC
54345307 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
54345328 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
54345350 G
1 G
54345351 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:54346322 original size:30 final size:30
Alignment explanation
Indices: 54346288--54346384 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54346278 TAAACTAAAA
54346288 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54346318 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54346348 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54346378 TGAGCTA
1 TGAGCTA
54346385 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54349049 original size:14 final size:14
Alignment explanation
Indices: 54349027--54349076 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
54349017 TAGAAAGAGG
* *
54349027 GGTACGAATGGAAT
1 GGTAGGAATGAAAT
*
54349041 GGTAGGAATGAAAG
1 GGTAGGAATGAAAT
**
54349055 GGTAGGAACAAAAT
1 GGTAGGAATGAAAT
54349069 GGTAGGAA
1 GGTAGGAA
54349077 CAAATTGGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.38, T:0.16
Consensus pattern (14 bp):
GGTAGGAATGAAAT
Found at i:54349077 original size:14 final size:14
Alignment explanation
Indices: 54349038--54349085 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54349028 GTACGAATGG
**
54349038 AATGGTAGGAATGA
1 AATGGTAGGAACAA
*
54349052 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
54349066 AATGGTAGGAACAA
1 AATGGTAGGAACAA
*
54349080 ATTGGT
1 AATGGT
54349086 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54351940 original size:30 final size:30
Alignment explanation
Indices: 54351869--54351951 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 30
54351859 CTTTTGTTTC
*
54351869 AATTTCTTTTTCATATTCTTTTTCACTCTCA
1 AATTTCTTTTTCAT-TTCTTTTTCAATCTCA
*
54351900 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATT-TCTTTTTCAATCTCA
*
54351929 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTCA-TTTCTTTTT
54351952 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 6 0.13
30 31 0.69
31 8 0.18
ACGTcount: A:0.14, C:0.20, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCATTTCTTTTTCAATCTCA
Found at i:54351951 original size:18 final size:18
Alignment explanation
Indices: 54351902--54351957 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54351892 CACTCTCAAA
* *
54351902 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
54351919 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
54351937 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
54351956 TT
1 TT
54351958 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:54351958 original size:12 final size:12
Alignment explanation
Indices: 54351927--54351951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54351917 TTTTTCAATC
54351927 TCATTTTCTTTT
1 TCATTTTCTTTT
54351939 TCATTTTCTTTT
1 TCATTTTCTTTT
54351951 T
1 T
54351952 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54352030 original size:5 final size:5
Alignment explanation
Indices: 54352020--54352076 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54352010 CTCTTGCCTC
*
54352020 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
54352067 TCTTT TCTTT
1 TCTTT TCTTT
54352077 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:54352060 original size:15 final size:14
Alignment explanation
Indices: 54352020--54352076 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54352010 CTCTTGCCTC
*
54352020 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
54352035 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
54352050 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
54352067 TCTTTTCTTT
1 TCTTTTCTTT
54352077 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:54352077 original size:21 final size:21
Alignment explanation
Indices: 54352020--54352087 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
54352010 CTCTTGCCTC
* *
54352020 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
54352041 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
54352062 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
54352082 CTCTTT
1 -TCTTT
54352088 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:54352941 original size:12 final size:13
Alignment explanation
Indices: 54352924--54352980 Score: 84
Period size: 13 Copynumber: 4.5 Consensus size: 13
54352914 CATTAAACAC
54352924 TTTTTTTTC-AGAT
1 TTTTTTTTCGA-AT
54352937 TTTTTTTTCGAA-
1 TTTTTTTTCGAAT
54352949 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
54352961 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
54352974 TTTTTTT
1 TTTTTTT
54352981 GAATTGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.07
12 16 0.39
13 21 0.51
14 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:54352952 original size:11 final size:11
Alignment explanation
Indices: 54352938--54352985 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
54352928 TTTTCAGATT
54352938 TTTTTTTCGAA
1 TTTTTTTCGAA
*
54352949 TTTTTTTTGAA
1 TTTTTTTCGAA
54352960 TTTTTTTTTCGAA
1 --TTTTTTTCGAA
*
54352973 TTTTTTTTGAA
1 TTTTTTTCGAA
54352984 TT
1 TT
54352986 GTATAACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 22 0.69
13 10 0.31
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:54352962 original size:24 final size:24
Alignment explanation
Indices: 54352924--54352985 Score: 106
Period size: 24 Copynumber: 2.5 Consensus size: 24
54352914 CATTAAACAC
*
54352924 TTTTTTTTCAGATTTTTTTTTCGAA
1 TTTTTTTTGA-ATTTTTTTTTCGAA
54352949 TTTTTTTTGAATTTTTTTTTCGAA
1 TTTTTTTTGAATTTTTTTTTCGAA
54352973 TTTTTTTTGAATT
1 TTTTTTTTGAATT
54352986 GTATAACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTTTTTTGAATTTTTTTTTCGAA
Found at i:54353246 original size:45 final size:45
Alignment explanation
Indices: 54353182--54353271 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
54353172 CAGAGAGAAA
54353182 GACATACTCCTAGTATATCTTCAAAGAAATCATTCAAGGAGTATT
1 GACATACTCCTAGTATATCTTCAAAGAAATCATTCAAGGAGTATT
*
54353227 GACATACTCTTAGTATATCTTCAAAGAAATCATTCAAGGAGTATT
1 GACATACTCCTAGTATATCTTCAAAGAAATCATTCAAGGAGTATT
54353272 CTTCACGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (45 bp):
GACATACTCCTAGTATATCTTCAAAGAAATCATTCAAGGAGTATT
Found at i:54355138 original size:26 final size:27
Alignment explanation
Indices: 54355109--54355159 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
54355099 TTGTAAAGAG
54355109 AAAACAAAG-AAAAGAAAAT-AAAAAGC
1 AAAA-AAAGAAAAAGAAAATGAAAAAGC
*
54355135 AAAAGAAGAAAAAGAAAATGAAAAA
1 AAAAAAAGAAAAAGAAAATGAAAAA
54355160 AAAAAGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 14 0.64
27 5 0.23
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (27 bp):
AAAAAAAGAAAAAGAAAATGAAAAAGC
Found at i:54355236 original size:12 final size:12
Alignment explanation
Indices: 54355228--54355252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54355218 TTTGAAAAGC
54355228 AAAAAGAAAATG
1 AAAAAGAAAATG
54355240 AAAAAGAAAATG
1 AAAAAGAAAATG
54355252 A
1 A
54355253 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54355249 original size:18 final size:18
Alignment explanation
Indices: 54355222--54355264 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54355212 AAAGCCTTTG
54355222 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54355241 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
54355259 AAAAGA
1 AAAAGA
54355265 GAACAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54355262 original size:30 final size:31
Alignment explanation
Indices: 54355228--54355309 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
54355218 TTTGAAAAGC
*
54355228 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
54355258 AAAAAGAGAA-CAAAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
54355288 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54355310 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 9 0.21
30 24 0.56
31 10 0.23
ACGTcount: A:0.66, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54360798 original size:13 final size:13
Alignment explanation
Indices: 54360780--54360813 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
54360770 CATAAATCAC
54360780 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
*
54360792 TTTTTTTTTGGAA
1 TTTTTTTTTCGAA
54360805 TTTTTTTTT
1 TTTTTTTTT
54360814 TCAAACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:54362417 original size:21 final size:22
Alignment explanation
Indices: 54362391--54362434 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
54362381 AAACGAGCTC
54362391 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
54362412 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
54362434 G
1 G
54362435 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:54363752 original size:30 final size:30
Alignment explanation
Indices: 54363677--54363753 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
54363667 TCAACTCGCG
* * **
54363677 AGCTAAACCTTAGCTCAACTTCAGCTTAGG
1 AGCTAAAGCTTAGCTCAACTTCAGCTCACA
** *
54363707 AG-TTTAGCCTCAGCTCAACTTCAGCTCACA
1 AGCTAAAG-CTTAGCTCAACTTCAGCTCACA
54363737 AGCTAAAGCTTAGCTCA
1 AGCTAAAGCTTAGCTCA
54363754 TTTTAGTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
29 2 0.06
30 30 0.86
31 3 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
AGCTAAAGCTTAGCTCAACTTCAGCTCACA
Found at i:54365097 original size:10 final size:10
Alignment explanation
Indices: 54365082--54365108 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54365072 TACTCCTTCA
54365082 AGCTCAAATC
1 AGCTCAAATC
54365092 AGCTCAAATC
1 AGCTCAAATC
54365102 AGCTCAA
1 AGCTCAA
54365109 CGAGCTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54371916 original size:10 final size:10
Alignment explanation
Indices: 54371901--54371927 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54371891 TACTCCTTCA
54371901 AGCTCAAATC
1 AGCTCAAATC
54371911 AGCTCAAATC
1 AGCTCAAATC
54371921 AGCTCAA
1 AGCTCAA
54371928 CGAGCTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54375109 original size:19 final size:19
Alignment explanation
Indices: 54375085--54375124 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54375075 AGCTCCCATG
54375085 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
54375104 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
54375123 TA
1 TA
54375125 TCAGCTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:54378260 original size:30 final size:29
Alignment explanation
Indices: 54378186--54378263 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
54378176 GAGTTAAGCT
* *
54378186 TTATCTCGTAAGCTAAAGTTGAGCTGAGA
1 TTATCTCGTAAGCTGAAGTTGAGCTAAGA
* * *
54378215 TTAAACTCCTAAGCTGAAGTTGAGCTAAGGC
1 TT-ATCTCGTAAGCTGAAGTTGAGCTAA-GA
*
54378246 TTATCTCGTGAGCTGAAG
1 TTATCTCGTAAGCTGAAG
54378264 GAGTGAGCTC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (29 bp):
TTATCTCGTAAGCTGAAGTTGAGCTAAGA
Found at i:54379547 original size:9 final size:10
Alignment explanation
Indices: 54379540--54379596 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54379530 AAGAGAAAAC
54379540 AAAGAAAAGA
1 AAAGAAAAGA
54379550 AAAGAAAAAGA
1 AAAG-AAAAGA
*
54379561 AAA-AGAAGAA
1 AAAGAAAAG-A
54379571 AAAGAAAATGA
1 AAAGAAAA-GA
54379582 AATA-AAAAGA
1 AA-AGAAAAGA
54379592 AAAGA
1 AAAGA
54379597 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 19 0.49
12 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54379550 original size:5 final size:5
Alignment explanation
Indices: 54379540--54379596 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54379530 AAGAGAAAAC
*
54379540 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
54379587 AAAGA AAAGA
1 AAAGA AAAGA
54379597 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54379676 original size:11 final size:12
Alignment explanation
Indices: 54379644--54379674 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
54379634 TTGAGAGAAC
54379644 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54379656 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54379668 TTGAAAA
1 TTGAAAA
54379675 GCAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:54379685 original size:12 final size:12
Alignment explanation
Indices: 54379677--54379701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54379667 TTTGAAAAGC
54379677 AAAAAGAAAATG
1 AAAAAGAAAATG
54379689 AAAAAGAAAATG
1 AAAAAGAAAATG
54379701 A
1 A
54379702 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54379698 original size:18 final size:18
Alignment explanation
Indices: 54379671--54379713 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54379661 AAAGCCTTTG
54379671 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54379690 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
54379708 AAAAGA
1 AAAAGA
54379714 GAACGGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54379711 original size:30 final size:31
Alignment explanation
Indices: 54379677--54379758 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
54379667 TTTGAAAAGC
*
54379677 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * * *
54379707 AAAAAGAGAACG-GAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
**
54379737 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54379759 TGAAACAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 7 0.17
30 25 0.62
31 8 0.20
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54384534 original size:31 final size:32
Alignment explanation
Indices: 54384493--54384552 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
54384483 ATTCGTTTCA
54384493 CACCTATGTTCACA-TGGCAAGACTATTCAGTT
1 CACCTATGTTCACATTGG-AAGACTATTCAGTT
*
54384525 CACCT-TGTTCACATTGGAAGACTCTTCA
1 CACCTATGTTCACATTGGAAGACTATTCA
54384553 ACATTCGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (32 bp):
CACCTATGTTCACATTGGAAGACTATTCAGTT
Found at i:54388702 original size:13 final size:13
Alignment explanation
Indices: 54388684--54388712 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54388674 AATAGTTGTG
54388684 TGTTATTTAATTA
1 TGTTATTTAATTA
54388697 TGTTATTTAATTA
1 TGTTATTTAATTA
54388710 TGT
1 TGT
54388713 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:54390842 original size:21 final size:21
Alignment explanation
Indices: 54390792--54390844 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
54390782 GTAAATCAGT
54390792 TGAGAGAAAAAGAAAAGAATGAA
1 TGAGA-AAAAAGAAAAGAA-GAA
*
54390815 TGTGAAAAAAGAAAAGAA-AA
1 TGAGAAAAAAGAAAAGAAGAA
54390835 TCGAGAAAAA
1 T-GAGAAAAA
54390845 GAATACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 7 0.26
22 13 0.48
23 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (21 bp):
TGAGAAAAAAGAAAAGAAGAA
Found at i:54394552 original size:30 final size:30
Alignment explanation
Indices: 54394457--54394553 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
54394447 AGCTCACTCC
* *
54394457 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* **
54394487 TAGCTCAACTTTAGCTTA-GCAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACG-AGCTAAAG-CT
*
54394517 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
54394547 TAGCTCA
1 TAGCTCA
54394554 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
29 3 0.06
30 40 0.77
31 9 0.17
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:54397269 original size:30 final size:30
Alignment explanation
Indices: 54397183--54397270 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
54397173 CTAGCTTACT
* *
54397183 TTCAACTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * ** *
54397213 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
54397243 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
54397271 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:54397795 original size:14 final size:14
Alignment explanation
Indices: 54397778--54397817 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
54397768 CGAATGGAAT
54397778 GGTAGGAACGAAAA-
1 GGTAGGAAC-AAAAC
54397792 GGTAGGAACAAAAC
1 GGTAGGAACAAAAC
*
54397806 GGTATGAACAAA
1 GGTAGGAACAAA
54397818 TTGGTCAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.50, C:0.10, G:0.30, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAC
Found at i:54398026 original size:45 final size:46
Alignment explanation
Indices: 54397973--54398064 Score: 177
Period size: 45 Copynumber: 2.0 Consensus size: 46
54397963 ACCCACTATC
54397973 TAACAAGATAGGAACCTCGATATGTTGAACGCCACACTACG-ATAG
1 TAACAAGATAGGAACCTCGATATGTTGAACGCCACACTACGAATAG
54398018 TAACAAGATAGGAACCTCGATATGTTGAACGCCACACTACGAATAG
1 TAACAAGATAGGAACCTCGATATGTTGAACGCCACACTACGAATAG
54398064 T
1 T
54398065 GATAAGTTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 41 0.89
46 5 0.11
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (46 bp):
TAACAAGATAGGAACCTCGATATGTTGAACGCCACACTACGAATAG
Found at i:54404328 original size:9 final size:10
Alignment explanation
Indices: 54404314--54404364 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 10
54404304 CATAAATCAC
54404314 TTTTTTTT-A
1 TTTTTTTTGA
54404323 TTTTTTTTGA
1 TTTTTTTTGA
54404333 TTTTTTTTTCGAA
1 -TTTTTTTT-G-A
54404346 TTTTTTTTTGA
1 -TTTTTTTTGA
54404357 TTTTTTTT
1 TTTTTTTT
54404365 AACTTGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.21
10 9 0.24
11 9 0.24
12 2 0.05
13 10 0.26
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:54404330 original size:11 final size:11
Alignment explanation
Indices: 54404314--54404364 Score: 70
Period size: 11 Copynumber: 4.6 Consensus size: 11
54404304 CATAAATCAC
54404314 TTTTTTTT-A-
1 TTTTTTTTGAT
54404323 TTTTTTTTGAT
1 TTTTTTTTGAT
54404334 TTTTTTTTCGAAT
1 TTTTTTTT-G-AT
54404347 TTTTTTTTGAT
1 TTTTTTTTGAT
54404358 TTTTTTT
1 TTTTTTT
54404365 AACTTGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
11 17 0.45
12 2 0.05
13 10 0.26
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:54404338 original size:12 final size:12
Alignment explanation
Indices: 54404323--54404364 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
54404313 CTTTTTTTTA
54404323 TTTTTTTTGATT
1 TTTTTTTTGATT
* *
54404335 TTTTTTTCGAAT
1 TTTTTTTTGATT
54404347 TTTTTTTTGATT
1 TTTTTTTTGATT
54404359 TTTTTT
1 TTTTTT
54404365 AACTTGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTTTTGATT
Found at i:54404745 original size:14 final size:14
Alignment explanation
Indices: 54404711--54404758 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
54404701 GTACGAATGG
**
54404711 AATGGTAGGAATGA
1 AATGGTAGGAACAA
*
54404725 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54404739 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
54404753 ATTGGT
1 AATGGT
54404759 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54408387 original size:9 final size:10
Alignment explanation
Indices: 54408380--54408427 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
54408370 AAGAGAAAAC
54408380 AAAGAAAAGA
1 AAAGAAAAGA
54408390 AAAGAAAAAGAA
1 AAAG-AAAAG-A
54408402 AAAGAAAACGA
1 AAAGAAAA-GA
54408413 AATA-AAAAGA
1 AA-AGAAAAGA
54408423 AAAGA
1 AAAGA
54408428 GAGGCAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 1 0.03
10 9 0.27
11 16 0.48
12 7 0.21
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54408390 original size:5 final size:5
Alignment explanation
Indices: 54408380--54408427 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
54408370 AAGAGAAAAC
54408380 AAAGA AAAGA AAAGAA AAAGAA AAAGA AAACGA AATA-A AAAGA AAAGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAA-GA AA-AGA AAAGA AAAGA
54408428 GAGGCAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 1 0.03
5 22 0.56
6 15 0.38
7 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:54408407 original size:22 final size:22
Alignment explanation
Indices: 54408380--54408425 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
54408370 AAGAGAAAAC
54408380 AAAGAAAA-GAAAAGAAAAAGAA
1 AAAGAAAACG-AAAGAAAAAGAA
*
54408402 AAAGAAAACGAAATAAAAAGAA
1 AAAGAAAACGAAAGAAAAAGAA
54408424 AA
1 AA
54408426 GAGAGGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAGAAAACGAAAGAAAAAGAA
Found at i:54408546 original size:30 final size:31
Alignment explanation
Indices: 54408496--54408566 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
54408486 TTTGAAAAGC
* *
54408496 AAAAAGAAA-ATGAGATTGAAAAAG-AGAATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAG-ATG
54408526 -AAAAGAAATTTGAGAGTGAAAAAGAAGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
54408556 AAAAAGAAATT
1 AAAAAGAAATT
54408567 GAAACAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 16 0.44
31 12 0.33
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
Found at i:54411093 original size:30 final size:30
Alignment explanation
Indices: 54411059--54411155 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
54411049 TAAACTAAAA
*
54411059 TGAGCTACGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54411089 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
54411119 TGAGCTAAGGTTTGGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54411149 TGAGCTA
1 TGAGCTA
54411156 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54412491 original size:30 final size:30
Alignment explanation
Indices: 54412396--54412492 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
54412386 AGCTCACTCC
* * *
54412396 TAGCTC-ACTTTCAACTCGCGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
54412426 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
54412456 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
54412486 TAGCTCA
1 TAGCTCA
54412493 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:54422791 original size:30 final size:30
Alignment explanation
Indices: 54422757--54422852 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54422747 TAAACTAAAA
54422757 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
54422787 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTGAGCTAAAGT
* *
54422817 TGAGCTAAGGTTTAGC-CGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54422846 TGAGCTA
1 TGAGCTA
54422853 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
29 13 0.25
30 36 0.71
31 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54423193 original size:14 final size:14
Alignment explanation
Indices: 54423146--54423193 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54423136 GTACGAATGG
*
54423146 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
54423160 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54423174 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
54423188 ATTGGT
1 AATGGT
54423194 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54425686 original size:10 final size:10
Alignment explanation
Indices: 54425671--54425697 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54425661 TACTCCTTCA
54425671 AGCTCAAATC
1 AGCTCAAATC
54425681 AGCTCAAATC
1 AGCTCAAATC
54425691 AGCTCAA
1 AGCTCAA
54425698 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54431829 original size:30 final size:30
Alignment explanation
Indices: 54431795--54431878 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
54431785 TAAACTAAAA
* *
54431795 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
54431825 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
54431855 TGAGC-AAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
54431879 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:54434609 original size:13 final size:13
Alignment explanation
Indices: 54434591--54434623 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
54434581 CATAAATCAC
54434591 TTTTTTTTC-GAA
1 TTTTTTTTCGGAA
54434603 TTTTTTTTCGGAA
1 TTTTTTTTCGGAA
54434616 TTTTTTTT
1 TTTTTTTT
54434624 TTCAAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (13 bp):
TTTTTTTTCGGAA
Found at i:54441517 original size:10 final size:10
Alignment explanation
Indices: 54441502--54441528 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54441492 TAAGTTGAAG
54441502 TTGAGCTGAT
1 TTGAGCTGAT
54441512 TTGAGCTGAT
1 TTGAGCTGAT
54441522 TTGAGCT
1 TTGAGCT
54441529 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:54455414 original size:30 final size:30
Alignment explanation
Indices: 54455380--54455476 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54455370 TAAACTAAAA
54455380 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54455410 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54455440 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54455470 TGAGCTA
1 TGAGCTA
54455477 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54458076 original size:10 final size:10
Alignment explanation
Indices: 54458061--54458087 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54458051 TACTCCTTCA
54458061 AGCTCAAATC
1 AGCTCAAATC
54458071 AGCTCAAATC
1 AGCTCAAATC
54458081 AGCTCAA
1 AGCTCAA
54458088 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54459766 original size:14 final size:14
Alignment explanation
Indices: 54459719--54459766 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54459709 GTACGAATGG
*
54459719 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
54459733 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54459747 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
54459761 ATTGGT
1 AATGGT
54459767 CGTTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54461019 original size:30 final size:29
Alignment explanation
Indices: 54460985--54461083 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 29
54460975 TAAACTAAAA
* *
54460985 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAACTCGTGAGCTGAAGT
* * * *
54461015 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAG-TTTAACTCGTGAGCTGAAGT
*
54461045 TGAGCTAAAGTTTACCTCGTGAGCTGAA-T
1 TGAGCT-AAGTTTAACTCGTGAGCTGAAGT
54461074 ATGAGCTAAG
1 -TGAGCTAAG
54461084 AGTGAGCTCG
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
29 4 0.07
30 49 0.89
31 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
TGAGCTAAGTTTAACTCGTGAGCTGAAGT
Found at i:54467761 original size:14 final size:14
Alignment explanation
Indices: 54467738--54467781 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54467728 GTAGAAAGAG
* *
54467738 GGGTACGAATGGAA
1 GGGTAGGAATGAAA
*
54467752 TGGTAGGAATGAAA
1 GGGTAGGAATGAAA
*
54467766 GGGTAGGAATAAAA
1 GGGTAGGAATGAAA
54467780 GG
1 GG
54467782 ATATGAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.41, T:0.16
Consensus pattern (14 bp):
GGGTAGGAATGAAA
Found at i:54482545 original size:11 final size:12
Alignment explanation
Indices: 54482513--54482545 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54482503 TGAGCTGTAG
54482513 AAACTTAATTAT
1 AAACTTAATTAT
*
54482525 AAACTGAATTA-
1 AAACTTAATTAT
54482536 AAACTTAATT
1 AAACTTAATT
54482546 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:54484378 original size:106 final size:106
Alignment explanation
Indices: 54484193--54484404 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
54484183 TAATGTTATG
54484193 CTGCCGAAATTGTGAGGTAAACTTTTCTTATATTTCGTTCAAAGATTCGTTTGGCGTTCCTAGCA
1 CTGCCGAAATTGTGAGGTAAACTTTTCTTATATTTCGTTCAAAGATTCGTTTGGCGTTCCTAGCA
54484258 TTCTAGTTGTGTCAACCGTGTTCTTTGTCGATTCCGAACTT
66 TTCTAGTTGTGTCAACCGTGTTCTTTGTCGATTCCGAACTT
54484299 CTGCCGAAATTGTGAGGTAAACTTTTCTTATATTTCGTTCAAAGATTCGTTTGGCGTTCCTAGCA
1 CTGCCGAAATTGTGAGGTAAACTTTTCTTATATTTCGTTCAAAGATTCGTTTGGCGTTCCTAGCA
54484364 TTCTAGTTGTGTCAACCGTGTTCTTTGTCGATTCCGAACTT
66 TTCTAGTTGTGTCAACCGTGTTCTTTGTCGATTCCGAACTT
54484405 ATCACTACTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (106 bp):
CTGCCGAAATTGTGAGGTAAACTTTTCTTATATTTCGTTCAAAGATTCGTTTGGCGTTCCTAGCA
TTCTAGTTGTGTCAACCGTGTTCTTTGTCGATTCCGAACTT
Found at i:54485383 original size:56 final size:52
Alignment explanation
Indices: 54485266--54485425 Score: 160
Period size: 56 Copynumber: 2.9 Consensus size: 52
54485256 CATAATCATG
* * *
54485266 ACATAACACGCCTCTCAACAGGGCTACATATGAGCACTCGGACCTAGCATGCATC
1 ACATTACACGCCTCTCAACAGGGCTACATA--AGCTC-CGGACCTAGCATGCACC
* *
54485321 ACATTACCACGCCTTTCAACAGGGCTACATAAGCTCCGGACCTAGCATGGACC
1 ACATTA-CACGCCTCTCAACAGGGCTACATAAGCTCCGGACCTAGCATGCACC
* * *
54485374 ACATAATTACATGCCTCTCAAC-GGGCCTACACAAGCTCCTGAACCTAGCATG
1 AC---ATTACACGCCTCTCAACAGGG-CTACATAAGCTCC-GGACCTAGCATG
54485426 TATCATGTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
53 17 0.19
54 7 0.08
55 28 0.31
56 38 0.42
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (52 bp):
ACATTACACGCCTCTCAACAGGGCTACATAAGCTCCGGACCTAGCATGCACC
Found at i:54486800 original size:10 final size:10
Alignment explanation
Indices: 54486785--54486811 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54486775 TACTCCTTCA
54486785 AGCTCAAATC
1 AGCTCAAATC
54486795 AGCTCAAATC
1 AGCTCAAATC
54486805 AGCTCAA
1 AGCTCAA
54486812 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54491940 original size:30 final size:30
Alignment explanation
Indices: 54491913--54492000 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
54491903 CTTGCTCATA
54491913 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
54491943 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
54491973 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
54492001 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:54495479 original size:53 final size:54
Alignment explanation
Indices: 54495374--54495529 Score: 181
Period size: 56 Copynumber: 2.8 Consensus size: 54
54495364 TCATGAATAG
* * *
54495374 CACGCCTCTCAACAGGGCTACATATGAGCACCCGGACCTAGCATGCATCAC-ATTA
1 CACGCCTCTCAACAGGGCTACATA--AGCTCCCGGACCTAGCATGTACCACAATTA
*
54495429 CCACGCCTCTCAACAGGG-TACATAAGCTCCCGGACCTAGCGTGTACCACATAATTA
1 -CACGCCTCTCAACAGGGCTACATAAGCTCCCGGACCTAGCATGTACCAC--AATTA
* * * *
54495485 CATGCCTCTCAACGGGGCTACACAAGCTCTCGGACCTAGCATGTA
1 CACGCCTCTCAACAGGGCTACATAAGCTCCCGGACCTAGCATGTA
54495530 TCATGTCATC
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
53 21 0.24
55 21 0.24
56 45 0.52
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (54 bp):
CACGCCTCTCAACAGGGCTACATAAGCTCCCGGACCTAGCATGTACCACAATTA
Found at i:54505012 original size:23 final size:23
Alignment explanation
Indices: 54504977--54505022 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
54504967 CTAGAAGAAA
54504977 AATCATGAATATCCATGAATGTG
1 AATCATGAATATCCATGAATGTG
54505000 AATCAT-AAGTATCCATGAATGTG
1 AATCATGAA-TATCCATGAATGTG
54505023 TAGCCCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (23 bp):
AATCATGAATATCCATGAATGTG
Found at i:54511621 original size:30 final size:31
Alignment explanation
Indices: 54511587--54511683 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54511577 AGCTCACTCC
*
54511587 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54511617 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54511647 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54511677 TAGCTCA
1 TAGCTCA
54511684 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54513414 original size:18 final size:18
Alignment explanation
Indices: 54513382--54513419 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
54513372 AAAAAAATTC
*
54513382 AAAAAAATTTCGAAAAGAA
1 AAAAAAATCTCGAAAA-AA
54513401 AAAAAAATCT-GAAAAAA
1 AAAAAAATCTCGAAAAAA
54513418 AA
1 AA
54513420 GTGTTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAATCTCGAAAAAA
Found at i:54514362 original size:21 final size:20
Alignment explanation
Indices: 54514328--54514370 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
54514318 ACATTCTTGT
54514328 AAAGAGAAAACAAAGAAAAGA
1 AAAGAGAAAACAAA-AAAAGA
*
54514349 AAAGA-AAAAGCAAAAGAAGA
1 AAAGAGAAAA-CAAAAAAAGA
54514369 AA
1 AA
54514371 GGAATAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAACAAAAAAAGA
Found at i:54521851 original size:30 final size:30
Alignment explanation
Indices: 54521766--54521862 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
54521756 TAAACTAAAA
* *
54521766 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * * *
54521796 TGAGTTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
54521826 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
54521855 ATGAGCTA
1 -TGAGCTA
54521863 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:54523222 original size:30 final size:31
Alignment explanation
Indices: 54523188--54523284 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54523178 AGCTCACTCC
*
54523188 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54523218 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54523248 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54523278 TAGCTCA
1 TAGCTCA
54523285 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54525808 original size:15 final size:16
Alignment explanation
Indices: 54525788--54525855 Score: 79
Period size: 15 Copynumber: 4.3 Consensus size: 16
54525778 AAGAGAAAAT
54525788 AAAGAAAAG-AAAAGA
1 AAAGAAAAGAAAAAGA
54525803 AAAGAAAAAGAAAAAGA
1 AAAG-AAAAGAAAAAGA
*
54525820 AAA-AGAAGAAAAAGA
1 AAAGAAAAGAAAAAGA
*
54525835 AAA-AGAAATAAAAAGA
1 AAAGA-AAAGAAAAAGA
54525851 AAAGA
1 AAAGA
54525856 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 19 0.41
16 17 0.37
17 10 0.22
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAGAAAAGAAAAAGA
Found at i:54525853 original size:6 final size:6
Alignment explanation
Indices: 54525788--54525842 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
54525778 AAGAGAAAAT
54525788 AAAG-A AAAG-A AAAG-A AAAGAA AAAGAA AAAGAA AAAG-- -AAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
54525830 AAAGAA AAAGAA A
1 AAAGAA AAAGAA A
54525843 TAAAAAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.07
5 14 0.30
6 29 0.63
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Done.