Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 171 of 259
Found at i:55560912 original size:28 final size:28
Alignment explanation
Indices: 55560872--55560953 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
55560862 CTATGTACAT
55560872 CACTTAGTGTGTGAGATATTGAGTATGG
1 CACTTAGTGTGTGAGATATTGAGTATGG
55560900 CACTTAGTGTGTGAGATATTGAGTATGG
1 CACTTAGTGTGTGAGATATTGAGTATGG
* * *
55560928 CTCTTAGTGTGCGAAATATTGAGTAT
1 CACTTAGTGTGTGAGATATTGAGTAT
55560954 TAAGTGGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.37
Consensus pattern (28 bp):
CACTTAGTGTGTGAGATATTGAGTATGG
Found at i:55576517 original size:55 final size:56
Alignment explanation
Indices: 55576454--55576568 Score: 180
Period size: 56 Copynumber: 2.1 Consensus size: 56
55576444 GTATTTTAGT
* * *
55576454 TGGTCAACCTAC-AAAATTCAAGAGA-AAGAAATTAACATCTTGCATGTAATTTAAG
1 TGGTCAACCTACAAAAATTAAAGAGAGAA-AAATCAACATCTTGCATATAATTTAAG
55576509 TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
1 TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
55576565 TGGT
1 TGGT
55576569 GTTGTAGTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 12 0.22
56 41 0.75
57 2 0.04
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (56 bp):
TGGTCAACCTACAAAAATTAAAGAGAGAAAAATCAACATCTTGCATATAATTTAAG
Found at i:55578000 original size:29 final size:29
Alignment explanation
Indices: 55577933--55578007 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
55577923 TGTTAGTAGT
*
55577933 TGGATTAAATTTTAAAATATGAAAAGTAA
1 TGGATTAAATTCTAAAATATGAAAAGTAA
* *
55577962 AGTGACTAAATTCCTAAAA-AT-AAAAGTACA
1 TG-GATTAAATT-CTAAAATATGAAAAGTA-A
55577992 TGGATTAAATTCTAAA
1 TGGATTAAATTCTAAA
55578008 TTTTTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 12 0.32
31 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGATTAAATTCTAAAATATGAAAAGTAA
Found at i:55579070 original size:29 final size:30
Alignment explanation
Indices: 55579008--55579069 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
55578998 AATCTATATC
* *
55579008 TTTATAATTTTTAAAGGATTAAATTAAATT
1 TTTATAATTTTTAAAGGATCAAAGTAAATT
*
55579038 TTTATAA-TTTTAAAGGGTCAAAGTACAATT
1 TTTATAATTTTTAAAGGATCAAAGTA-AATT
55579068 TT
1 TT
55579070 ACCTTTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGATCAAAGTAAATT
Found at i:55579369 original size:42 final size:42
Alignment explanation
Indices: 55579310--55579395 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
55579300 TTCTTTTATC
55579310 AATATTACACATGATTAGTCAACCAGAAAATAACTTACTTAG
1 AATATTACACATGATTAGTCAACCAGAAAATAACTTACTTAG
55579352 AATATTACACATGATTAGTCAACCAGAAAATAACTTACTTAG
1 AATATTACACATGATTAGTCAACCAGAAAATAACTTACTTAG
55579394 AA
1 AA
55579396 AATAAAGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (42 bp):
AATATTACACATGATTAGTCAACCAGAAAATAACTTACTTAG
Found at i:55584262 original size:32 final size:31
Alignment explanation
Indices: 55584218--55584289 Score: 135
Period size: 32 Copynumber: 2.3 Consensus size: 31
55584208 AAACTAAGGT
55584218 ATGTATGCAGTGATAATTCAAAGGAATGATG
1 ATGTATGCAGTGATAATTCAAAGGAATGATG
55584249 ATGTTATGCAGTGATAATTCAAAGGAATGATG
1 ATG-TATGCAGTGATAATTCAAAGGAATGATG
55584281 ATGTATGCA
1 ATGTATGCA
55584290 ATAGATGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 9 0.22
32 31 0.77
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (31 bp):
ATGTATGCAGTGATAATTCAAAGGAATGATG
Found at i:55585282 original size:37 final size:37
Alignment explanation
Indices: 55585228--55585318 Score: 148
Period size: 36 Copynumber: 2.5 Consensus size: 37
55585218 TATCTTCTCC
55585228 TCTTTTTAAATTCTTTTTTCAACAACCCAAGATTATCT
1 TCTTTTTAAATT-TTTTTTCAACAACCCAAGATTATCT
* *
55585266 T-TTTTTAAAATTTTTTTCAACAACCCGAGATTATCT
1 TCTTTTTAAATTTTTTTTCAACAACCCAAGATTATCT
55585302 TCTTTTTAAATTTTTTT
1 TCTTTTTAAATTTTTTT
55585319 CTCCTATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 25 0.51
37 23 0.47
38 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.03, T:0.53
Consensus pattern (37 bp):
TCTTTTTAAATTTTTTTTCAACAACCCAAGATTATCT
Found at i:55589824 original size:50 final size:50
Alignment explanation
Indices: 55589765--55589918 Score: 130
Period size: 63 Copynumber: 2.8 Consensus size: 50
55589755 GTATTCTTTT
55589765 GAAACCTTACATTTACCACGATCAACCTTCGAAATTTGTTCGGTTATTTC
1 GAAACCTTACATTTACCACGATCAACCTTCGAAATTTGTTCGGTTATTTC
* * ** *
55589815 GAAACCTTACATTCTTTTGAAACCTTAC-TTTAAGTTATCCAAATATCATGTTTCGGTTATTTC
1 GAAACCTTACA----TTT---ACC--ACGATCAACCT-TCGAAAT-T--TGTT-CGGTTATTTC
55589878 GAAACCTTACATTTACCACGATCAACCTTCGAAATTTGTTC
1 GAAACCTTACATTTACCACGATCAACCTTCGAAATTTGTTC
55589919 ATTGGGGTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 30
0.66 0.08 0.25
Matches are distributed among these distances:
50 12 0.15
51 4 0.05
53 1 0.01
54 11 0.14
55 4 0.05
56 3 0.04
57 3 0.04
58 4 0.05
59 11 0.14
60 1 0.01
62 4 0.05
63 21 0.27
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (50 bp):
GAAACCTTACATTTACCACGATCAACCTTCGAAATTTGTTCGGTTATTTC
Found at i:55599242 original size:20 final size:22
Alignment explanation
Indices: 55599192--55599247 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
55599182 TAGTCATATA
* * *
55599192 ATAAATTATTAATATAATAAAT
1 ATAATTTATTATTTTAATAAAT
55599214 ATAATTTATTATTTTAATAAAT
1 ATAATTTATTATTTTAATAAAT
55599236 -T-ATTTATTATTT
1 ATAATTTATTATTT
55599248 CAATTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 11 0.35
21 1 0.03
22 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTTATTATTTTAATAAAT
Found at i:55599286 original size:14 final size:14
Alignment explanation
Indices: 55599255--55599293 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
55599245 TTTCAATTTT
55599255 ATTTT-AATAATAA
1 ATTTTAAATAATAA
55599268 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
55599282 ATTTTAAATAAT
1 ATTTTAAATAAT
55599294 GTTATTCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:55599828 original size:14 final size:14
Alignment explanation
Indices: 55599809--55599846 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
55599799 CTAGAAAAGT
55599809 AAATCATTTTCCAG
1 AAATCATTTTCCAG
55599823 AAATCA-TTTCCAG
1 AAATCATTTTCCAG
*
55599836 AAGTCATTTTC
1 AAATCATTTTC
55599847 AATGAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:55601252 original size:27 final size:28
Alignment explanation
Indices: 55601220--55601461 Score: 277
Period size: 27 Copynumber: 8.9 Consensus size: 28
55601210 AAGTACTCCC
55601220 GATTTACAGAATTACCGTTTTACCCTCA
1 GATTTACAGAATTACCGTTTTACCCTCA
* * *
55601248 G-TTTATAAAATTACTGTTTTACCCTC-
1 GATTTACAGAATTACCGTTTTACCCTCA
55601274 GATTTACAGAATTACCGTTTTACCCTCA
1 GATTTACAGAATTACCGTTTTACCCTCA
* *
55601302 G-TTTACAGAATTACTGCTTTACCCTC-
1 GATTTACAGAATTACCGTTTTACCCTCA
* *
55601328 GATTTATAAAATTACCGTTTTACCCTC-
1 GATTTACAGAATTACCGTTTTACCCTCA
** * * *
55601355 GATTTGTAAAATTACCATTTTACCCT-T
1 GATTTACAGAATTACCGTTTTACCCTCA
*
55601382 GATTTACAGAATTACTAG-TTTACCCTCA
1 GATTTACAGAATTAC-CGTTTTACCCTCA
* *
55601410 G-TTTACAAAATTATCGTTTTACCCTC-
1 GATTTACAGAATTACCGTTTTACCCTCA
55601436 GATTTACAGAATTACCGTTTTACCCT
1 GATTTACAGAATTACCGTTTTACCCT
55601462 TAATTGTGCA
Statistics
Matches: 181, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.02
27 174 0.96
28 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (28 bp):
GATTTACAGAATTACCGTTTTACCCTCA
Found at i:55601257 original size:54 final size:54
Alignment explanation
Indices: 55601219--55601461 Score: 337
Period size: 54 Copynumber: 4.5 Consensus size: 54
55601209 AAAGTACTCC
*
55601219 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAAAATTACCGTTTTACCCT
* * * *
55601273 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGCTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAAAATTACCGTTTTACCCT
* * * *
55601327 CGATTTATAAAATTACCGTTTTACCCTC-GATTTGTAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAG-TTTATAAAATTACCGTTTTACCCT
* * * *
55601381 TGATTTACAGAATTACTAG-TTTACCCTCAGTTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTAC-CGTTTTACCCTCAGTTTATAAAATTACCGTTTTACCCT
55601435 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
55601462 TAATTGTGCA
Statistics
Matches: 164, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.01
54 160 0.98
55 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (54 bp):
CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAAAATTACCGTTTTACCCT
Found at i:55601462 original size:81 final size:80
Alignment explanation
Indices: 55601220--55601462 Score: 339
Period size: 81 Copynumber: 3.0 Consensus size: 80
55601210 AAGTACTCCC
* *
55601220 GATTTACAGAATTACCGTTTTACCCTCAGTTTATAAAATTACTGTTTTACCCTCGATTTACAGAA
1 GATTTACAGAATTACTGCTTTACCCTCAGTTTATAAAATTAC-GTTTTACCCTCGATTTACAGAA
55601285 TTACCGTTTTACCC-T
65 TTACCGTTTTACCCTT
* ** *
55601300 CAGTTTACAGAATTACTGCTTTACCCTC-GATTTATAAAATTACCGTTTTACCCTCGATTTGTAA
1 GA-TTTACAGAATTACTGCTTTACCCTCAG-TTTATAAAATTA-CGTTTTACCCTCGATTTACAG
*
55601364 AATTACCATTTTACCCTT
63 AATTACCGTTTTACCCTT
*
55601382 GATTTACAGAATTACTAG-TTTACCCTCAGTTTACAAAATTATCGTTTTACCCTCGATTTACAGA
1 GATTTACAGAATTACT-GCTTTACCCTCAGTTTATAAAATTA-CGTTTTACCCTCGATTTACAGA
55601446 ATTACCGTTTTACCCTT
64 ATTACCGTTTTACCCTT
55601463 AATTGTGCAA
Statistics
Matches: 143, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
80 2 0.01
81 136 0.95
82 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (80 bp):
GATTTACAGAATTACTGCTTTACCCTCAGTTTATAAAATTACGTTTTACCCTCGATTTACAGAAT
TACCGTTTTACCCTT
Found at i:55601501 original size:27 final size:27
Alignment explanation
Indices: 55601471--55601666 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 27
55601461 TTAATTGTGC
*
55601471 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
55601498 AATTTCCGAAATACCCATATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * **
55601525 AATTACTAAAATACCCTTATAGAATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55601552 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55601579 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55601606 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
55601633 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
55601660 AATTACC
1 AATTACC
55601667 ATTTTGCCCC
Statistics
Matches: 143, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 143 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:55601903 original size:27 final size:26
Alignment explanation
Indices: 55601865--55601947 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
55601855 CGGAGGAAGC
55601865 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
55601892 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
55601918 GTATTTGGTGACTTTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
55601945 GTT
1 GTT
55601948 GACCGATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.20
27 40 0.80
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:55602067 original size:22 final size:22
Alignment explanation
Indices: 55602035--55602093 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
55602025 CCCGTTATTA
*
55602035 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
55602057 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
55602079 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
55602094 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:55602280 original size:27 final size:27
Alignment explanation
Indices: 55602258--55602331 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
55602248 TAGGTGGGTT
*
55602258 TGCCACATTATCTG-ATTCTGGTGACTC
1 TGCCACAATATCTGTA-TCTGGTGACTC
*
55602285 TGCCACAATATCTGTATCTGGTGACTT
1 TGCCACAATATCTGTATCTGGTGACTC
* *
55602312 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
55602332 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGACTC
Found at i:55602458 original size:6 final size:6
Alignment explanation
Indices: 55602449--55602646 Score: 151
Period size: 6 Copynumber: 32.7 Consensus size: 6
55602439 TTGCATTCAC
* * *
55602449 ATTCTG ATTCTG ATTCTG -TCACATA ATTTTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
55602498 -TTACTA ATACTG ATTCTG ATTCTA ATTCTG -TTACTG ATTCTG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * *
55602546 ATTCTG -TCACCTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG AT--TCTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
* *
55602595 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCTC ATTTTG
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG
55602643 ATTC
1 ATTC
55602647 CAATTTTGAT
Statistics
Matches: 153, Mismatches: 22, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
5 12 0.08
6 128 0.84
7 10 0.07
8 3 0.02
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:55602514 original size:30 final size:30
Alignment explanation
Indices: 55602449--55602635 Score: 233
Period size: 30 Copynumber: 6.4 Consensus size: 30
55602439 TTGCATTCAC
* **
55602449 ATTCTGATTCTGATTCTGTCACATAATTTTG
1 ATTCTGATTCTGATTCTGTTAC-TAATACTG
55602480 ATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
*
55602510 ATTCTGATTCTAATTCTG----T--TACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
55602534 ATTCTGATTCTGATTCTGTCACCTAATATTG
1 ATTCTGATTCTGATTCTGTTA-CTAATACTG
*
55602565 ATTCTGATTCTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
55602595 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
55602625 ATTCTGATTCT
1 ATTCTGATTCT
55602636 CATTTTGATT
Statistics
Matches: 139, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
24 22 0.16
26 1 0.01
29 1 0.01
30 70 0.50
31 45 0.32
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:55602548 original size:85 final size:85
Alignment explanation
Indices: 55602449--55602635 Score: 338
Period size: 85 Copynumber: 2.2 Consensus size: 85
55602439 TTGCATTCAC
*
55602449 ATTCTGATTCTGATTCTGTCACATAATTTTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACATAATATTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
55602514 TGATTCTAATTCTGTTACTG
66 TGATTCTAATTCTGTTACTG
* *
55602534 ATTCTGATTCTGATTCTGTCACCTAATATTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACATAATATTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
*
55602599 TGATTCTGATTCTGTTACTG
66 TGATTCTAATTCTGTTACTG
55602619 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
55602636 CATTTTGATT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (85 bp):
ATTCTGATTCTGATTCTGTCACATAATATTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TGATTCTAATTCTGTTACTG
Found at i:55605726 original size:11 final size:11
Alignment explanation
Indices: 55605712--55605740 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
55605702 TATAAAATAA
55605712 TTAAATTGTAC
1 TTAAATTGTAC
55605723 TTAAATTGTAC
1 TTAAATTGTAC
55605734 TTAAATT
1 TTAAATT
55605741 ATTAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (11 bp):
TTAAATTGTAC
Found at i:55613167 original size:27 final size:27
Alignment explanation
Indices: 55613130--55613318 Score: 234
Period size: 27 Copynumber: 7.0 Consensus size: 27
55613120 GTTATTTGAT
* *
55613130 CGTAATACCCCTGTAGGGTAAAATGAT
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
55613157 TGTAATGCCCCTGTAAGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* * *
55613184 TGAAATGCCCATGTAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
55613211 CGTAATGCCCCTTTAGGGTAAAATAAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* **
55613238 CGTAATACCCCTAAAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
55613265 AGTAATGCCCCTATAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
55613292 CGTAATACCCCTGTATGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
55613319 GATTATGCCC
Statistics
Matches: 139, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
CGTAATGCCCCTGTAGGGTAAAATGAC
Found at i:55613533 original size:26 final size:26
Alignment explanation
Indices: 55613503--55613555 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
55613493 GGCTTTGCCA
* *
55613503 CATTACTGTTTCTGGCAGCTATGCTG
1 CATTACTATTACTGGCAGCTATGCTG
* *
55613529 CATTATTATTACTGGCAGCTTTGCTG
1 CATTACTATTACTGGCAGCTATGCTG
55613555 C
1 C
55613556 GATTTCGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (26 bp):
CATTACTATTACTGGCAGCTATGCTG
Found at i:55623131 original size:32 final size:32
Alignment explanation
Indices: 55623095--55623179 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
55623085 CCCATTACAG
* * * *
55623095 TATCAATTGGGCGTAGCCCATCTCAGAATCAA
1 TATCAGTTGGGCCTAGCCCATATCAGAACCAA
* *
55623127 TATCAGTTAGGCCTAGCCTATATCAGAACCAA
1 TATCAGTTGGGCCTAGCCCATATCAGAACCAA
55623159 TATCAGTTGGGCCTAGCCCAT
1 TATCAGTTGGGCCTAGCCCAT
55623180 TTCAATATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (32 bp):
TATCAGTTGGGCCTAGCCCATATCAGAACCAA
Found at i:55624267 original size:18 final size:18
Alignment explanation
Indices: 55624234--55624345 Score: 93
Period size: 18 Copynumber: 6.2 Consensus size: 18
55624224 AGTTTCATTT
55624234 AGTAAC-ATTCAATTATTC
1 AGTAACAATT-AATTATTC
* *
55624252 AGTAGCAATTAGTTATTC
1 AGTAACAATTAATTATTC
* * **
55624270 AGTAACAATCATTTGCTC
1 AGTAACAATTAATTATTC
*
55624288 AGTAGC-ATTCAATTATTC
1 AGTAACAATT-AATTATTC
*
55624306 AGTAACAATCAATTATTC
1 AGTAACAATTAATTATTC
* * *
55624324 AGTAACAGTTAGTCATTC
1 AGTAACAATTAATTATTC
55624342 AGTA
1 AGTA
55624346 CTTTTATTTA
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
17 2 0.03
18 66 0.90
19 5 0.07
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (18 bp):
AGTAACAATTAATTATTC
Found at i:55624290 original size:36 final size:36
Alignment explanation
Indices: 55624234--55624345 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 36
55624224 AGTTTCATTT
* *
55624234 AGTAACATTCAATTATTCAGTAGCAATTAGTTATTC
1 AGTAACAATCAATTACTCAGTAGCAATTAGTTATTC
* * *
55624270 AGTAACAATCATTTGCTCAGTAGC-ATTCAATTATTC
1 AGTAACAATCAATTACTCAGTAGCAATT-AGTTATTC
* * * *
55624306 AGTAACAATCAATTATTCAGTAACAGTTAGTCATTC
1 AGTAACAATCAATTACTCAGTAGCAATTAGTTATTC
55624342 AGTA
1 AGTA
55624346 CTTTTATTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
35 3 0.05
36 57 0.92
37 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (36 bp):
AGTAACAATCAATTACTCAGTAGCAATTAGTTATTC
Found at i:55624344 original size:54 final size:54
Alignment explanation
Indices: 55624228--55624345 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
55624218 TTTATCAGTT
* * * * *
55624228 TCATTTAGTAACATTCAATTATTCAGTAGCAATTAGTTATTCAGTAACAATCAT
1 TCATTCAGTAACATTCAATTATTCAGTAACAATCAATTATTCAGTAACAATCAG
*** * * *
55624282 TTGCTCAGTAGCATTCAATTATTCAGTAACAATCAATTATTCAGTAACAGTTAG
1 TCATTCAGTAACATTCAATTATTCAGTAACAATCAATTATTCAGTAACAATCAG
55624336 TCATTCAGTA
1 TCATTCAGTA
55624346 CTTTTATTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (54 bp):
TCATTCAGTAACATTCAATTATTCAGTAACAATCAATTATTCAGTAACAATCAG
Found at i:55624704 original size:17 final size:17
Alignment explanation
Indices: 55624672--55624704 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55624662 TTCCATATTA
55624672 CATTTCAATTTCAATTT
1 CATTTCAATTTCAATTT
55624689 CATTCTCAATTT-AATT
1 CATT-TCAATTTCAATT
55624705 ACAACTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (17 bp):
CATTTCAATTTCAATTT
Found at i:55625010 original size:135 final size:132
Alignment explanation
Indices: 55624769--55625037 Score: 314
Period size: 135 Copynumber: 2.0 Consensus size: 132
55624759 TACATATTCA
*
55624769 TCATTCAACTCAATTTTCATTCAATTCAACAATAACACTTAACTTATAATTTACTTACCATATAC
1 TCATTCAACTCAATTTTCATTCAATTCAACAATAACACTTAACTTATAATTTACTTACCATATAA
* * * *
55624834 ATAAATTAATTTAACATTTAATGAATAAATAAATAATTTGAATTATAGTAATACAAACACGT-AT
66 ATAAATAAATTTAAAATTTAATAAATAAATAAATAACTTGAATTATAGTAATACAAAC-CGTAAT
55624898 TTC
130 TTC
* * * * * *
55624901 TCATTCAATTCAATTTTCTAAATTCAATTCAATAA-AATTACTTACCTTA-ATATTTGCTTACTA
1 TCATTCAACTCAATTTTC---ATTCAATTCAACAATAA-CACTTAACTTATA-ATTTACTTACCA
* *
55624964 TA-AAATAAATAAATTTAAAATTAATACTAAAT-AATAAATAACTTGAATTATAGTAATATAAAC
61 TATAAATAAATAAATTTAAAATT--TAATAAATAAATAAATAACTTGAATTATAGTAATACAAAC
55625027 CGTAATTTC
124 CGTAATTTC
55625036 TC
1 TC
55625038 GAATTATTCT
Statistics
Matches: 116, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
132 17 0.15
134 23 0.20
135 70 0.60
136 6 0.05
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.39
Consensus pattern (132 bp):
TCATTCAACTCAATTTTCATTCAATTCAACAATAACACTTAACTTATAATTTACTTACCATATAA
ATAAATAAATTTAAAATTTAATAAATAAATAAATAACTTGAATTATAGTAATACAAACCGTAATT
TC
Found at i:55625278 original size:13 final size:15
Alignment explanation
Indices: 55625252--55625284 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
55625242 CATTTACTTT
55625252 ATATATATTATAATA
1 ATATATATTATAATA
55625267 ATATA-ATT-TAATA
1 ATATATATTATAATA
55625280 ATATA
1 ATATA
55625285 CTTATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATTATAATA
Found at i:55625386 original size:4 final size:4
Alignment explanation
Indices: 55625377--55625415 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
55625367 TGTCAAACTT
*
55625377 TTAA TTAA TTAA TTAA TTAA TTTACA TTAT TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA -TTA-A TTAA TTAA TTAA T
55625416 ATAAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.77
5 6 0.19
6 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:55629965 original size:17 final size:17
Alignment explanation
Indices: 55629940--55629973 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55629930 TTTAATTCAA
*
55629940 CATATATCAATCAAAAT
1 CATAAATCAATCAAAAT
*
55629957 CATAAATCAATTAAAAT
1 CATAAATCAATCAAAAT
55629974 TTATCCTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (17 bp):
CATAAATCAATCAAAAT
Found at i:55637872 original size:24 final size:25
Alignment explanation
Indices: 55637830--55637877 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
55637820 ACACAAACGC
55637830 AGCTCTTCATGAGCGTCCTGATATA
1 AGCTCTTCATGAGCGTCCTGATATA
*
55637855 AGCTCTT-ATGAGCTTCCTGATAT
1 AGCTCTTCATGAGCGTCCTGATAT
55637878 GGCTCGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTCTTCATGAGCGTCCTGATATA
Found at i:55642416 original size:38 final size:39
Alignment explanation
Indices: 55642365--55642441 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
55642355 CCATCTCCGT
* *
55642365 CTAGCCCAACACACC-GTGTGGGGATAAAATCGACCCAC
1 CTAGCCCAACACACCAGTATGGGGATAAAATCAACCCAC
* *
55642403 CTAGCCCTACACACCAAGTATTGGGATAAAATCAACCCA
1 CTAGCCCAACACACC-AGTATGGGGATAAAATCAACCCA
55642442 TCCAACTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 14 0.42
40 19 0.58
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.16
Consensus pattern (39 bp):
CTAGCCCAACACACCAGTATGGGGATAAAATCAACCCAC
Found at i:55642918 original size:17 final size:17
Alignment explanation
Indices: 55642896--55642928 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55642886 GTGTGGTTCA
55642896 CCTGTGTGGCCCACACG
1 CCTGTGTGGCCCACACG
55642913 CCTGTGTGGCCCACAC
1 CCTGTGTGGCCCACAC
55642929 AGCCCAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.42, G:0.27, T:0.18
Consensus pattern (17 bp):
CCTGTGTGGCCCACACG
Found at i:55645817 original size:40 final size:40
Alignment explanation
Indices: 55645762--55645838 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
55645752 ATCATGGAAC
55645762 ATTTACCTAAACCATTATCATGGAACATTTACCTAACAAT
1 ATTTACCTAAACCATTATCATGGAACATTTACCTAACAAT
*
55645802 ATTTACCTAATCCATTATCATGGAACATTTACCTAAC
1 ATTTACCTAAACCATTATCATGGAACATTTACCTAAC
55645839 CCATTATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (40 bp):
ATTTACCTAAACCATTATCATGGAACATTTACCTAACAAT
Found at i:55647448 original size:22 final size:19
Alignment explanation
Indices: 55647423--55647464 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
55647413 TGATAATAAC
55647423 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
55647445 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
55647464 T
1 T
55647465 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:55647455 original size:16 final size:15
Alignment explanation
Indices: 55647423--55647461 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
55647413 TGATAATAAC
55647423 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
55647439 TTATTATAATATATAT
1 TAATTATAAT-TATAT
55647455 TAATTAT
1 TAATTAT
55647462 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:55648051 original size:15 final size:15
Alignment explanation
Indices: 55648031--55648062 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55648021 CATTCGATCA
55648031 AATTGAATCGAATCG
1 AATTGAATCGAATCG
55648046 AATTGAATCGAATCG
1 AATTGAATCGAATCG
55648061 AA
1 AA
55648063 AATTTTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (15 bp):
AATTGAATCGAATCG
Found at i:55649099 original size:9 final size:9
Alignment explanation
Indices: 55649085--55649121 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55649075 TATAGTTTGA
55649085 TATTCGAAT
1 TATTCGAAT
55649094 TATTCGAAT
1 TATTCGAAT
*
55649103 TATTCGAGT
1 TATTCGAAT
*
55649112 TATTTGAAT
1 TATTCGAAT
55649121 T
1 T
55649122 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55649188 original size:9 final size:9
Alignment explanation
Indices: 55649174--55649206 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
55649164 ATTCGAGTTG
55649174 ACTCGAATA
1 ACTCGAATA
*
55649183 ACTCGATTA
1 ACTCGAATA
55649192 ACTCGAATA
1 ACTCGAATA
55649201 ACTCGA
1 ACTCGA
55649207 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:55649197 original size:18 final size:18
Alignment explanation
Indices: 55649174--55649208 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
55649164 ATTCGAGTTG
55649174 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
55649192 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
55649209 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:55649512 original size:25 final size:26
Alignment explanation
Indices: 55649456--55649513 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
55649446 ATTTTTCTCC
* *
55649456 TAAA-TTTCAAATTTATTTAGTTAAT
1 TAAATTTTCAAATTTATTGAATTAAT
55649481 TAAATTTTC-AATTTATTGAATT-AT
1 TAAATTTTCAAATTTATTGAATTAAT
55649505 TAATATTTT
1 TAA-ATTTT
55649514 ATGCAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 5 0.17
25 20 0.69
26 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
TAAATTTTCAAATTTATTGAATTAAT
Found at i:55652429 original size:20 final size:21
Alignment explanation
Indices: 55652406--55652446 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55652396 ATTAATTTTA
55652406 TAATAT-TTTTTCATAAATTT
1 TAATATATTTTTCATAAATTT
* *
55652426 TAATTTATTTTTGATAAATTT
1 TAATATATTTTTCATAAATTT
55652447 GCACAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TAATATATTTTTCATAAATTT
Found at i:55656161 original size:28 final size:28
Alignment explanation
Indices: 55656119--55656183 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
55656109 ATGATTCAAA
55656119 AAATT-CAACGATCATATTACAACAGTC
1 AAATTCCAACGATCATATTACAACAGTC
* * *
55656146 AGATTCCAACGGTCATATTATAACAGTC
1 AAATTCCAACGATCATATTACAACAGTC
55656174 AAATTCCAAC
1 AAATTCCAAC
55656184 AACTATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (28 bp):
AAATTCCAACGATCATATTACAACAGTC
Found at i:55656191 original size:28 final size:28
Alignment explanation
Indices: 55656130--55656197 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
55656120 AATTCAACGA
* * **
55656130 TCATATTACAACAGTCAGATTCCAACGG
1 TCATATTATAACAGTCAAATTCCAACAC
55656158 TCATATTATAACAGTCAAATTCCAACAAC
1 TCATATTATAACAGTCAAATTCCAAC-AC
*
55656187 T-ATATTGTAAC
1 TCATATTATAAC
55656198 GAAACGATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (28 bp):
TCATATTATAACAGTCAAATTCCAACAC
Found at i:55662687 original size:41 final size:41
Alignment explanation
Indices: 55662511--55662798 Score: 319
Period size: 41 Copynumber: 7.0 Consensus size: 41
55662501 TTGTAAAACA
* * * * * *
55662511 CAGAGCAATAGCGGCGTTTTTGTTAACATGCCACTAAAA-A
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
* * * * *
55662551 CAGAGCAATAGCGACGTTTTTTGTTAAAACACCGCTAAAA-A
1 CAGAGCAATAGCGGCG-CTTTTGATAAAACGCCGCTAAAAGT
* ** * *
55662592 CAGATCAATAGCGGTACTTTTGGTAAAACTCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
* * *
55662633 CGGAGCAATAGCGGCGCTTTTGGTAAAATGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
*
55662674 CAGAGCAATAGCGGCGCTTCTGATAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
* * * * *
55662715 CGGAGCAGTAGTGGCGCTTCTGATAAAACGTCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
*
55662756 CGGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
1 CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
55662797 CA
1 CA
55662799 TATAATCCCT
Statistics
Matches: 214, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
40 35 0.16
41 179 0.84
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (41 bp):
CAGAGCAATAGCGGCGCTTTTGATAAAACGCCGCTAAAAGT
Found at i:55662911 original size:53 final size:54
Alignment explanation
Indices: 55662810--55662922 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 54
55662800 ATAATCCCTA
* * * *
55662810 AAACCCCTAAACCCCAAAAAATCATGAACACTAATCTATAACCCCTAAAATACT
1 AAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
* * * ** *
55662864 AAACCCCTAAA-CCCTAAAAACCCTAAACCCTAAACTATAACTTCTAAAACCCT
1 AAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
55662917 AAACCC
1 AAACCC
55662923 AAAAAACATC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
53 38 0.78
54 11 0.22
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.18
Consensus pattern (54 bp):
AAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCTAAAACACT
Found at i:55663093 original size:15 final size:15
Alignment explanation
Indices: 55663049--55663099 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
55663039 CGGTTTAATA
*
55663049 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* * *
55663063 TCTATAGTTTAGGGT
1 TTTATGGTTTAAGGT
55663078 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
55663093 TTAATGG
1 TTTATGG
55663100 CCATGGGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:55663642 original size:7 final size:7
Alignment explanation
Indices: 55663632--55663711 Score: 74
Period size: 7 Copynumber: 11.3 Consensus size: 7
55663622 CATTAAACCG
55663632 AAATAAA
1 AAATAAA
55663639 AAAT--A
1 AAATAAA
*
55663644 AACTCAAA
1 AAAT-AAA
55663652 AAATAAA
1 AAATAAA
*
55663659 AATTAAA
1 AAATAAA
55663666 AAATAAAA
1 AAAT-AAA
*
55663674 AAATTAA
1 AAATAAA
* *
55663681 AATTTAA
1 AAATAAA
55663688 AAATAAA
1 AAATAAA
55663695 AAATTAAA
1 AAA-TAAA
55663703 AAATAAA
1 AAATAAA
55663710 AA
1 AA
55663712 CTTAAAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 4 0.07
7 38 0.63
8 18 0.30
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:55663654 original size:13 final size:13
Alignment explanation
Indices: 55663632--55663673 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
55663622 CATTAAACCG
55663632 AAAT-AAAAAATA
1 AAATCAAAAAATA
*
55663644 AACTCAAAAAATAA
1 AAATCAAAAAAT-A
*
55663658 AAATTAAAAAATA
1 AAATCAAAAAATA
55663671 AAA
1 AAA
55663674 AAATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.44
14 11 0.44
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATCAAAAAATA
Found at i:55663667 original size:8 final size:8
Alignment explanation
Indices: 55663656--55663734 Score: 85
Period size: 8 Copynumber: 10.4 Consensus size: 8
55663646 CTCAAAAAAT
55663656 AAAAATTA
1 AAAAATTA
*
55663664 AAAAATAA
1 AAAAATTA
55663672 AAAAATT-
1 AAAAATTA
*
55663679 -AAAATTT
1 AAAAATTA
55663686 AAAAA-TA
1 AAAAATTA
55663693 AAAAATTA
1 AAAAATTA
55663701 AAAAA-TA
1 AAAAATTA
*
55663708 AAAACTTA
1 AAAAATTA
*
55663716 AAAATTTA
1 AAAAATTA
*
55663724 AAAATTTA
1 AAAAATTA
55663732 AAA
1 AAA
55663735 TTTAATATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
6 6 0.10
7 12 0.19
8 44 0.71
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAATTA
Found at i:55663690 original size:37 final size:37
Alignment explanation
Indices: 55663649--55663736 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
55663639 AAATAAACTC
55663649 AAAAAATAAAAATTAAAAAATAAAAAAATT-AAAATTT
1 AAAAAATAAAAATTAAAAAAT-AAAAAATTAAAAATTT
*
55663686 -AAAAATAAAAAATTAAAAAATAAAAACTTAAAAATTT
1 AAAAAAT-AAAAATTAAAAAATAAAAAATTAAAAATTT
* *
55663723 AAAAATTTAAAATT
1 AAAAAATAAAAATT
55663737 TAATATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
36 13 0.29
37 27 0.60
38 5 0.11
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (37 bp):
AAAAAATAAAAATTAAAAAATAAAAAATTAAAAATTT
Found at i:55663734 original size:15 final size:15
Alignment explanation
Indices: 55663649--55663739 Score: 87
Period size: 15 Copynumber: 6.1 Consensus size: 15
55663639 AAATAAACTC
* *
55663649 AAAAAATAAAAATTA
1 AAAAATTAAAAATTT
* *
55663664 AAAAATAAAAAAATT
1 AAAAATTAAAAATTT
* *
55663679 AAAATTTAAAAA-TA
1 AAAAATTAAAAATTT
*
55663693 AAAAATTAAAAA-AT
1 AAAAATTAAAAATTT
55663707 AAAAACTTAAAAATTT
1 AAAAA-TTAAAAATTT
*
55663723 AAAAATTTAAAATTT
1 AAAAATTAAAAATTT
55663738 AA
1 AA
55663740 TATTTTAGTC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
14 17 0.27
15 39 0.63
16 6 0.10
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAAAATTT
Found at i:55663824 original size:18 final size:16
Alignment explanation
Indices: 55663803--55663840 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
55663793 TCCAAAAGAG
55663803 AAAAATAAAAAATATGTT
1 AAAAATAAAAAA-AT-TT
55663821 AAAAATAAAAAAATTT
1 AAAAATAAAAAAATTT
55663837 AAAA
1 AAAA
55663841 TTAATCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATAAAAAAATTT
Found at i:55670151 original size:19 final size:19
Alignment explanation
Indices: 55670129--55670169 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
55670119 TTTATTGATA
55670129 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
55670147 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
55670166 TTTT
1 TTTT
55670170 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:55675778 original size:30 final size:30
Alignment explanation
Indices: 55675744--55675804 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
55675734 TTCCCGAGCC
55675744 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
55675774 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
55675804 T
1 T
55675805 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:55676587 original size:68 final size:67
Alignment explanation
Indices: 55676515--55676664 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
55676505 CATCATGTGT
* * * *
55676515 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
55676577 ATGTAG
62 ATGTAG
** * *
55676583 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
55676648 AG
66 AG
55676650 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
55676665 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:55676620 original size:64 final size:64
Alignment explanation
Indices: 55676539--55676722 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
55676529 AGACATTATG
* *
55676539 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
55676603 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
55676668 AA
63 AA
* * * *
55676670 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
55676723 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:55678804 original size:50 final size:50
Alignment explanation
Indices: 55678573--55678807 Score: 269
Period size: 50 Copynumber: 4.7 Consensus size: 50
55678563 AGGTCACGTA
* *
55678573 TGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGTTAGGTCGTATG
1 TGTAGTACTAAGTGCAGGCTACTACGAGTACCAGATTGTTAGGTCGTATG
* * ** * * *
55678623 TGTAGTACTAAGTGCAGGCTACTATGCGTACC-GATAACTTCGATC-AAGTG
1 TGTAGTACTAAGTGCAGGCTACTACGAGTACCAGAT-TGTTAGGTCGTA-TG
* * * * *
55678673 TGCAGTACTAAGTGCAGGCTACTAC-ATGTATCAGATGGTTAGGTCATGTG
1 TGTAGTACTAAGTGCAGGCTACTACGA-GTACCAGATTGTTAGGTCGTATG
* *
55678723 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGAGTACCAGATTGTTAGGTCGTATG
*
55678773 TGTAGTACTAAGTGCAGGCTACTATGAGTACCAGA
1 TGTAGTACTAAGTGCAGGCTACTACGAGTACCAGA
55678808 GAGCTTCGGT
Statistics
Matches: 152, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
49 4 0.03
50 145 0.95
51 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTAGTACTAAGTGCAGGCTACTACGAGTACCAGATTGTTAGGTCGTATG
Found at i:55684510 original size:2 final size:2
Alignment explanation
Indices: 55684503--55684532 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55684493 AATACTTCTT
*
55684503 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55684533 AAAATGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:55698088 original size:25 final size:25
Alignment explanation
Indices: 55698057--55698110 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
55698047 TGGGTCGTAT
*
55698057 GAGCTTC-CCGTTATATGGCTCAAAA
1 GAGCTTCTCAGTTATAT-GCTCAAAA
* *
55698082 GAGCTTCTCATTTATATGCTCAAAT
1 GAGCTTCTCAGTTATATGCTCAAAA
55698107 GAGC
1 GAGC
55698111 AATCCCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (25 bp):
GAGCTTCTCAGTTATATGCTCAAAA
Found at i:55702331 original size:25 final size:23
Alignment explanation
Indices: 55702294--55702339 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
55702284 TTTGTTTTAA
*
55702294 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
55702317 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
55702340 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:55705981 original size:180 final size:180
Alignment explanation
Indices: 55705659--55706024 Score: 660
Period size: 180 Copynumber: 2.0 Consensus size: 180
55705649 GGACCAATTG
*
55705659 TATAATTTAACCTAAAATTTTTATTTGAAATTATGATTTAACGTGTCACGTCAACTTACTATTAT
1 TATAATTTAACCTAAAATTTTTATTTGAAATTATGATTTAACGTGTCACGTCAACTTACCATTAT
* *
55705724 ACCGTTAATGGCAATTAACACTCAATGACTAAAATGTTACAACACGATAACGTAAGTGACTAAAA
66 ACCGTTAATGACAATTAACACTCAATGACTAAAATGTTACAACACGATAACGTAAATGACTAAAA
* * *
55705789 TATTATATGAGAGAAACAAAAGTGATTATTTTGATAGTTTACCCATGTAA
131 TATAACATGAGAGAAACAAAAATGATTATTTTGATAGTTTACCCATGTAA
55705839 TATAATTTAACCTAAAATTTTTATTTGAAATTATGATTTAACGTGTCACGTCAACTTACCATTAT
1 TATAATTTAACCTAAAATTTTTATTTGAAATTATGATTTAACGTGTCACGTCAACTTACCATTAT
*
55705904 ACCGTTAATGACAATTAACACTCAATGACTAAAATGTTACAACACGATAACGTAAATGATTAAAA
66 ACCGTTAATGACAATTAACACTCAATGACTAAAATGTTACAACACGATAACGTAAATGACTAAAA
*
55705969 TGTAACATGAGAGAAACAAAAATGATTATTTTGATAGTTTACCCATGTAA
131 TATAACATGAGAGAAACAAAAATGATTATTTTGATAGTTTACCCATGTAA
55706019 TATAAT
1 TATAAT
55706025 ACACTATACT
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 178 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (180 bp):
TATAATTTAACCTAAAATTTTTATTTGAAATTATGATTTAACGTGTCACGTCAACTTACCATTAT
ACCGTTAATGACAATTAACACTCAATGACTAAAATGTTACAACACGATAACGTAAATGACTAAAA
TATAACATGAGAGAAACAAAAATGATTATTTTGATAGTTTACCCATGTAA
Found at i:55715173 original size:44 final size:45
Alignment explanation
Indices: 55715120--55715222 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 45
55715110 TGTCTTTGAC
* * *
55715120 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
55715164 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
55715210 ATGGACTTACATG
1 ATGGACTTACATG
55715223 CCTCATTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 33 0.65
46 18 0.35
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:55722585 original size:46 final size:44
Alignment explanation
Indices: 55722482--55722586 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
55722472 TGTCTTTGAC
** * * **
55722482 ATGGACTTACATGAATTATTCCTGTCTCCAATTCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
55722526 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
55722572 ATGGACTTACATGGC
1 ATGGACTTACATGGC
55722587 GCATTTCTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 32 0.62
46 20 0.38
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:55729653 original size:43 final size:43
Alignment explanation
Indices: 55729606--55729740 Score: 107
Period size: 43 Copynumber: 3.1 Consensus size: 43
55729596 TTTTCCCTCT
55729606 TTCCCACTTCTTTTATTCTTTTGCTGCCTAAATTCTCTTACTC
1 TTCCCACTTCTTTTATTCTTTTGCTGCCTAAATTCTCTTACTC
* ** * * * * *
55729649 TTCCCCTCTGTCCGTT-TTCTTTCT-CTTCTTTCAA-TC-GTTCCTC
1 TT-CCCACT-TCTTTTATTCTTT-TGCTGC-CTAAATTCTCTTACTC
* *
55729692 TTTCCCACTTATTTTATTCTTTTGCTGCCGAAATTCTCTTACTC
1 -TTCCCACTTCTTTTATTCTTTTGCTGCCTAAATTCTCTTACTC
55729736 TTCCC
1 TTCCC
55729741 CTCTGTCCGT
Statistics
Matches: 65, Mismatches: 18, Indels: 18
0.64 0.18 0.18
Matches are distributed among these distances:
42 6 0.09
43 28 0.43
44 23 0.35
45 8 0.12
ACGTcount: A:0.11, C:0.33, G:0.06, T:0.50
Consensus pattern (43 bp):
TTCCCACTTCTTTTATTCTTTTGCTGCCTAAATTCTCTTACTC
Found at i:55729669 original size:44 final size:44
Alignment explanation
Indices: 55729621--55729757 Score: 120
Period size: 44 Copynumber: 3.1 Consensus size: 44
55729611 ACTTCTTTTA
55729621 TTCTTTTGCTGCCTAAATTCTCTTACTCTTCCCCTCTGTCCGTT
1 TTCTTTTGCTGCCTAAATTCTCTTACTCTTCCCCTCTGTCCGTT
* * * * * * * ***
55729665 TTCTTTCT-CTTCTTTCAA-TC-GTTCCTCTTTCCCACT-TATTTT
1 TTCTTT-TGCTGC-CTAAATTCTCTTACTCTTCCCCTCTGTCCGTT
*
55729707 ATTCTTTTGCTGCCGAAATTCTCTTACTCTTCCCCTCTGTCCGTT
1 -TTCTTTTGCTGCCTAAATTCTCTTACTCTTCCCCTCTGTCCGTT
55729752 TTCTTT
1 TTCTTT
55729758 CTCTTCTTTC
Statistics
Matches: 65, Mismatches: 21, Indels: 14
0.65 0.21 0.14
Matches are distributed among these distances:
42 6 0.09
43 23 0.35
44 29 0.45
45 7 0.11
ACGTcount: A:0.09, C:0.32, G:0.07, T:0.51
Consensus pattern (44 bp):
TTCTTTTGCTGCCTAAATTCTCTTACTCTTCCCCTCTGTCCGTT
Found at i:55729707 original size:87 final size:87
Alignment explanation
Indices: 55729601--55729777 Score: 327
Period size: 87 Copynumber: 2.0 Consensus size: 87
55729591 ATTCTTTTTC
* *
55729601 CCTCTTTCCCACTTCTTTTATTCTTTTGCTGCCTAAATTCTCTTACTCTTCCCCTCTGTCCGTTT
1 CCTCTTTCCCACTTATTTTATTCTTTTGCTGCCGAAATTCTCTTACTCTTCCCCTCTGTCCGTTT
55729666 TCTTTCTCTTCTTTCAATCGTT
66 TCTTTCTCTTCTTTCAATCGTT
55729688 CCTCTTTCCCACTTATTTTATTCTTTTGCTGCCGAAATTCTCTTACTCTTCCCCTCTGTCCGTTT
1 CCTCTTTCCCACTTATTTTATTCTTTTGCTGCCGAAATTCTCTTACTCTTCCCCTCTGTCCGTTT
*
55729753 TCTTTCTCTTCTTTCAATTGTT
66 TCTTTCTCTTCTTTCAATCGTT
55729775 CCT
1 CCT
55729778 ATTGTTTATC
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.10, C:0.33, G:0.06, T:0.51
Consensus pattern (87 bp):
CCTCTTTCCCACTTATTTTATTCTTTTGCTGCCGAAATTCTCTTACTCTTCCCCTCTGTCCGTTT
TCTTTCTCTTCTTTCAATCGTT
Found at i:55734888 original size:55 final size:55
Alignment explanation
Indices: 55734811--55734945 Score: 155
Period size: 55 Copynumber: 2.5 Consensus size: 55
55734801 ATGTAGGCCC
* * * * * *
55734811 ACGCCCATGTT-AGTTTAACAGGTTCGACCACGGTTTCTTGGCACTGGCGTGTCGA
1 ACGCCCACGTTGA-TTTGACAGGTTCGACCACGGGTTCTAGACACGGGCGTGTCGA
* *
55734866 ACGCCCGCGTTGATTTGACAGGTTCGGCCACGGGTTCTAGACACGGGCGTGTCGA
1 ACGCCCACGTTGATTTGACAGGTTCGACCACGGGTTCTAGACACGGGCGTGTCGA
* * *
55734921 ACGCCCATGTTGTTTTGGCAGGTTC
1 ACGCCCACGTTGATTTGACAGGTTC
55734946 ACCCATGGCC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
55 66 0.99
56 1 0.01
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.27
Consensus pattern (55 bp):
ACGCCCACGTTGATTTGACAGGTTCGACCACGGGTTCTAGACACGGGCGTGTCGA
Found at i:55737103 original size:46 final size:46
Alignment explanation
Indices: 55737002--55737089 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
55736992 TGTAACCCGC
* * * *
55737002 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
55737048 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
55737090 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:55744577 original size:46 final size:46
Alignment explanation
Indices: 55744476--55744563 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
55744466 TGTAACCCGC
* * * *
55744476 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTCCCAT
* * *
55744522 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTC
55744564 AACCATCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:55765483 original size:142 final size:141
Alignment explanation
Indices: 55765227--55765679 Score: 527
Period size: 142 Copynumber: 3.2 Consensus size: 141
55765217 AGGGGTTGCA
* *
55765227 ATTTTTCACCTGCAAGCCTTAATATGACAGTTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAG
1 ATTTTTCACCTGTAAGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAG
* * * * *
55765292 GCTGTGGTTTTTTACCTACAAGCCTTAATATGACAGTTAGGAGTTTGTAACTTTCACTAATTGTG
66 GCTGTGGTTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCACTAACTGTG
55765357 TTGGAAGCTACG
131 TTGGAAGCT-CG
* * * *
55765369 ATTTTTCACCTGTGACCCTTAATATGACAGCTG-GAAGTTTGTAACTCTCG-TCAACTATATTAG
1 ATTTTTCACCTGTAAGCCTTAATATGACAGCTGAG-AGTTTGTAACTCTCGCT-AACTGTGTTAG
* * ** *
55765432 AGGCTGTGGTTTTTCACTTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGGTAACTA
64 AGGCTGTGGTTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCACTAACTG
*
55765497 TGTTGGAGGCTGCG
129 TGTTGGAAGCT-CG
* * * * * *
55765511 ATTTTTCACTTATAAGCCTTAATATGATAGCTGAGAGTTTGGAACTCTTGCTAACTGTGTTGGAG
1 ATTTTTCACCTGTAAGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAG
* * ** * * *
55765576 GCTGCGGTCTTTCACCTGCAAGATTTAATATGATAGTTGGGAGTTTCTAACTCT-AGCTAACTGT
66 GCTGTGGTTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCA-CTAACTGT
55765640 GTTGGAAGCT-G
130 GTTGGAAGCTCG
* *
55765651 TAGTTTTTCACCTGTGAGCTTTAATATGA
1 -A-TTTTTCACCTGTAAGCCTTAATATGA
55765680 TAGTTGGGTG
Statistics
Matches: 259, Mismatches: 45, Indels: 14
0.81 0.14 0.04
Matches are distributed among these distances:
140 1 0.00
141 3 0.01
142 253 0.98
143 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (141 bp):
ATTTTTCACCTGTAAGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAG
GCTGTGGTTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCACTAACTGTG
TTGGAAGCTCG
Found at i:55765606 original size:213 final size:213
Alignment explanation
Indices: 55765228--55765687 Score: 521
Period size: 213 Copynumber: 2.2 Consensus size: 213
55765218 GGGGTTGCAA
* * * *
55765228 TTTTTCACCTGCAAGCCTTAATATGACAGTTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAGG
1 TTTTTCACCTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGCTAACTATGTTAGAGG
* * * * * *
55765293 CTGTGGTTTTTTACCTACAAGCCTTAATATGACAGTTAGGAGTTTGTAACTTTCACTAATTGTGT
66 CTGCGATTTTTCACCTACAAGCCTTAATATGACAGTGAGGAGTTTGGAACTTTCACTAACTGTGT
* ** * * *
55765358 TGGAAGCTACGATTTTTCACCTGTGACCCTTAATATGACAGCTGGAAGTTTGTAACTCTCG-TCA
131 TGGAAGCTACGATCTTTCACCTGCAACACTTAATATGACAGCTGGAAGTTTCTAACTCTAGCT-A
* *
55765422 ACTATATTAGAGGCTGTGG
195 ACTATATTAGAAGCTGTAG
* * *
55765441 TTTTTCACTTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGGTAACTATGTTGGAGG
1 TTTTTCACCTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGCTAACTATGTTAGAGG
* * * *
55765506 CTGCGATTTTTCACTTATAAGCCTTAATATGATAGCTGA-GAGTTTGGAACTCTT-GCTAACTGT
66 CTGCGATTTTTCACCTACAAGCCTTAATATGACAG-TGAGGAGTTTGGAACT-TTCACTAACTGT
* * * * * * * *
55765569 GTTGGAGGCTGCGGTCTTTCACCTGCAAGATTTAATATGATAGTTGGGAGTTTCTAACTCTAGCT
129 GTTGGAAGCTACGATCTTTCACCTGCAACACTTAATATGACAGCTGGAAGTTTCTAACTCTAGCT
* * *
55765634 AACTGTGTTGGAAGCTGTAG
194 AACTATATTAGAAGCTGTAG
* * *
55765654 TTTTTCACCTGTGAGCTTTAATATGATAGTTGGG
1 TTTTTCACCTGCGAGCCTTAATATGACAGTTGGG
55765688 TGACTAGGGG
Statistics
Matches: 204, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
213 199 0.98
214 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (213 bp):
TTTTTCACCTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGCTAACTATGTTAGAGG
CTGCGATTTTTCACCTACAAGCCTTAATATGACAGTGAGGAGTTTGGAACTTTCACTAACTGTGT
TGGAAGCTACGATCTTTCACCTGCAACACTTAATATGACAGCTGGAAGTTTCTAACTCTAGCTAA
CTATATTAGAAGCTGTAG
Found at i:55765686 original size:71 final size:71
Alignment explanation
Indices: 55765228--55765687 Score: 472
Period size: 71 Copynumber: 6.5 Consensus size: 71
55765218 GGGGTTGCAA
* *
55765228 TTTTTCACCTGCAAGCCTTAATATGACAGTTGAGAGTTTGTAACTCTCGCTAACTGTGTTAGAGG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
55765293 CTGTGG
66 CTGTGG
* * * * * * *
55765299 TTTTTTACCTACAAGCCTTAATATGACAGTTAGGAGTTTGTAACTTTCACTAATTGTGTTGGAAG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
** *
55765364 CTACGA
66 CTGTGG
** * * * * * *
55765370 TTTTTCACCTGTGACCCTTAATATGACAGCTGGAAGTTTGTAACTCTCG-TCAACTATATTAGAG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCT-AACTGTGTTGGAG
55765434 GCTGTGG
65 GCTGTGG
* * * * *
55765441 TTTTTCACTTGCGAGCCTTAATATGACAGTTGGGAGTTTGTAACTATCGGTAACTATGTTGGAGG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
* *
55765506 CTGCGA
66 CTGTGG
* ** * * * * *
55765512 TTTTTCACTTATAAGCCTTAATATGATAGCTGAGAGTTTGGAACTCTTGCTAACTGTGTTGGAGG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
*
55765577 CTGCGG
66 CTGTGG
* ** * * * *
55765583 TCTTTCACCTGCAAGATTTAATATGATAGTTGGGAGTTTCTAACTCTAGCTAACTGTGTTGGAAG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
*
55765648 CTGTAG
66 CTGTGG
** * *
55765654 TTTTTCACCTGTGAGCTTTAATATGATAGTTGGG
1 TTTTTCACCTGCAAGCCTTAATATGACAGTTGGG
55765688 TGACTAGGGG
Statistics
Matches: 317, Mismatches: 70, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
70 1 0.00
71 315 0.99
72 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (71 bp):
TTTTTCACCTGCAAGCCTTAATATGACAGTTGGGAGTTTGTAACTCTCGCTAACTGTGTTGGAGG
CTGTGG
Found at i:55770409 original size:12 final size:12
Alignment explanation
Indices: 55770379--55770418 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
55770369 TACTCTCAAG
*
55770379 TTTTATTTTGTTA
1 TTTTATTTT-TTC
55770392 TTTTATTTTTTC
1 TTTTATTTTTTC
*
55770404 TTTTATTTTTAC
1 TTTTATTTTTTC
55770416 TTT
1 TTT
55770419 CGAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTC
Found at i:55773485 original size:48 final size:48
Alignment explanation
Indices: 55773414--55773796 Score: 682
Period size: 48 Copynumber: 8.0 Consensus size: 48
55773404 CAAGATAAAT
* *
55773414 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
55773462 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
55773510 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAATTATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
55773558 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
55773606 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
55773654 ATATGTATATGTGGTAAAGCCGAATGGCTA-TGTGAAATA--TATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
55773699 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
55773747 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
55773795 AT
1 AT
55773797 GTGTGTATAT
Statistics
Matches: 322, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
45 36 0.11
46 9 0.03
47 9 0.03
48 268 0.83
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:55773992 original size:37 final size:37
Alignment explanation
Indices: 55773937--55774039 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
55773927 GGAAATATAT
55773937 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
55773974 TCCGGGTAAGACCTGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
55774011 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
55774040 GGACTATTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:55775534 original size:119 final size:120
Alignment explanation
Indices: 55775319--55775612 Score: 491
Period size: 119 Copynumber: 2.5 Consensus size: 120
55775309 TGAGAGTTAT
* *
55775319 ATATATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGA
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGA
* * *
55775384 GCATTCGTGCTAGTGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTA
66 GCATTCATGCTAGTAATGTATCCAGGCTAAGTTCCGAAGAGCATTCGTGCTAGTA
*
55775438 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATCCGGGCTAAGTTCCGAAGA
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGA
* *
55775503 GCATTCATGCTAGTAATGTATCCAGGTTAAGTTCCGAAGCGCATTCGTGCTAGTA
66 GCATTCATGCTAGTAATGTATCCAGGCTAAGTTCCGAAGAGCATTCGTGCTAGTA
* *
55775558 ATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAA
55775613 ACCTCGAAGG
Statistics
Matches: 163, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 89 0.55
120 74 0.45
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (120 bp):
ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGA
GCATTCATGCTAGTAATGTATCCAGGCTAAGTTCCGAAGAGCATTCGTGCTAGTA
Found at i:55775621 original size:40 final size:40
Alignment explanation
Indices: 55775326--55775612 Score: 477
Period size: 40 Copynumber: 7.2 Consensus size: 40
55775316 TATATATATT
* *
55775326 CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
*
55775366 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
*
55775406 CGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTAATATATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
55775445 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
*
55775485 CGGGCTAAGTTCCGAAGAGCATTCATGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
* * *
55775525 CAGGTTAAGTTCCGAAGCGCATTCGTGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
* *
55775565 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
55775605 CGGGCTAA
1 CGGGCTAA
55775613 ACCTCGAAGG
Statistics
Matches: 232, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
39 37 0.16
40 195 0.84
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
Found at i:55775736 original size:28 final size:27
Alignment explanation
Indices: 55775700--55775799 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
55775690 AGTAGTTGAG
*
55775700 GCACTATGTGTGTGAGTTCTTCAATCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
** *
55775728 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
55775756 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
55775785 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
55775800 AATCAGTCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 36 0.59
29 25 0.41
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:55775794 original size:57 final size:57
Alignment explanation
Indices: 55775639--55775806 Score: 210
Period size: 57 Copynumber: 2.9 Consensus size: 57
55775629 TGTGGAGTTA
* * * * ** * *
55775639 TGAGGCATTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTACGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* **
55775696 TGAGGCACTATGTGTGTGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* * *
55775753 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
55775807 CAGTGGGCAC
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 94 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:55779385 original size:48 final size:48
Alignment explanation
Indices: 55779328--55779656 Score: 604
Period size: 48 Copynumber: 6.9 Consensus size: 48
55779318 ATATAATATG
55779328 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
55779376 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGAATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
55779424 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
55779472 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
55779520 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
55779568 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
55779616 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
55779657 GTGTGTATAT
Statistics
Matches: 272, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 272 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:55779850 original size:37 final size:37
Alignment explanation
Indices: 55779799--55779899 Score: 168
Period size: 37 Copynumber: 2.7 Consensus size: 37
55779789 AAATATATTT
55779799 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
* *
55779836 TGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
55779873 CGGGTAAGACCCGAT-AGCTACGTGTGG
1 CGGGTAAGACCCGATGA-CTACGTGTGG
55779900 GGACTATTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
Found at i:55781514 original size:17 final size:17
Alignment explanation
Indices: 55781492--55781525 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55781482 TTAATTTCCC
*
55781492 ATATATTATTTATTTTA
1 ATATATTATTTACTTTA
*
55781509 ATATATTCTTTACTTTA
1 ATATATTATTTACTTTA
55781526 GATTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTATTTACTTTA
Found at i:55781845 original size:26 final size:27
Alignment explanation
Indices: 55781816--55781871 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
55781806 TTTAAACTCC
*
55781816 TTTACATATTATTTATTTTAAA-TATT
1 TTTACATATTATTTACTTTAAACTATT
* *
55781842 TTTATATTTTATTTACTTTAAACTATT
1 TTTACATATTATTTACTTTAAACTATT
55781869 TTT
1 TTT
55781872 TTATGTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTACATATTATTTACTTTAAACTATT
Found at i:55782142 original size:25 final size:24
Alignment explanation
Indices: 55782104--55782166 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
55782094 ATATTATTTT
55782104 ATTGTTTTGAATATTAATGATTTTTAA
1 ATTGTTTT--ATATTAATGA-TTTTAA
* *
55782131 ATTGTTTTATATTATTTATTTTAA
1 ATTGTTTTATATTAATGATTTTAA
55782155 ATTGCTTTTATA
1 ATTG-TTTTATA
55782167 GTATCTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 10 0.30
25 15 0.45
27 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (24 bp):
ATTGTTTTATATTAATGATTTTAA
Found at i:55782180 original size:25 final size:24
Alignment explanation
Indices: 55782128--55782180 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
55782118 TAATGATTTT
* * *
55782128 TAAATTGTTTTATATTATTTATTT
1 TAAATTGTTTTATAGTATCTATTC
*
55782152 TAAATTGCTTTTATAGTATCTCTTC
1 TAAATTG-TTTTATAGTATCTATTC
55782177 TAAA
1 TAAA
55782181 CCTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.57
Consensus pattern (24 bp):
TAAATTGTTTTATAGTATCTATTC
Found at i:55800990 original size:29 final size:29
Alignment explanation
Indices: 55800948--55801008 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
55800938 GTACTCACAA
55800948 ATGGTGGTAGGGGCAATATCAATGTTAGC
1 ATGGTGGTAGGGGCAATATCAATGTTAGC
55800977 ATGGTGGTAGGGGCAATATCAATGTTAGC
1 ATGGTGGTAGGGGCAATATCAATGTTAGC
55801006 ATG
1 ATG
55801009 TCTGATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (29 bp):
ATGGTGGTAGGGGCAATATCAATGTTAGC
Found at i:55801315 original size:25 final size:27
Alignment explanation
Indices: 55801267--55801318 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
55801257 TAAATAAAAA
* *
55801267 ATTTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
55801294 ATTTAAAAAACATAA-AAA-CAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
55801319 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 13 0.57
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTAAAAAACATAATAAATCAAATAT
Found at i:55801330 original size:22 final size:22
Alignment explanation
Indices: 55801296--55801347 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
55801286 TCAAATATAT
55801296 TTAAAA-AACATAAAAACAAATA
1 TTAAAACAACATAAAAA-AAATA
*
55801318 TTAAAACAA-ATAAAAATAATA
1 TTAAAACAACATAAAAAAAATA
*
55801339 CTAAAACAA
1 TTAAAACAA
55801348 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 13 0.48
23 2 0.07
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (22 bp):
TTAAAACAACATAAAAAAAATA
Found at i:55801332 original size:21 final size:20
Alignment explanation
Indices: 55801300--55801347 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
55801290 ATATATTTAA
* *
55801300 AAAACATAAAAACA-AATATT
1 AAAACA-AAAAAAATAATACT
55801320 AAAACAAATAAAAATAATACT
1 AAAACAAA-AAAAATAATACT
55801341 AAAACAA
1 AAAACAA
55801348 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAACAAAAAAAATAATACT
Found at i:55810190 original size:28 final size:27
Alignment explanation
Indices: 55810126--55810277 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
55810116 TTATTAAGCC
* *
55810126 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
55810153 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
55810181 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
55810208 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
55810236 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
55810263 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55810278 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:55810210 original size:55 final size:55
Alignment explanation
Indices: 55810126--55810302 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
55810116 TTATTAAGCC
* * *
55810126 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
55810181 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
55810236 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
55810292 CGCACACTTAG
1 CGCACACTTAG
55810303 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:55818189 original size:28 final size:27
Alignment explanation
Indices: 55818125--55818276 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
55818115 TTATTAAGTC
* *
55818125 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
55818152 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
55818180 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
55818207 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
55818235 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
55818262 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55818277 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:55818209 original size:55 final size:55
Alignment explanation
Indices: 55818125--55818301 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
55818115 TTATTAAGTC
* * *
55818125 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
55818180 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
55818235 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
55818291 CGCACACTTAG
1 CGCACACTTAG
55818302 CGTCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:55839225 original size:20 final size:19
Alignment explanation
Indices: 55839202--55839243 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55839192 AGATTATATA
55839202 TATTAT-ATTATATAATTGAT
1 TATTATAATTAT-TAATTG-T
55839222 TATTATAATTATTAATTGT
1 TATTATAATTATTAATTGT
55839241 TAT
1 TAT
55839244 GGTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTATAATTATTAATTGT
Found at i:55840314 original size:40 final size:40
Alignment explanation
Indices: 55840270--55840351 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
55840260 AATTTATGGG
* *
55840270 TTACTAAATATTGTTTTGAATACGGAATTGAACTGTGAAA
1 TTACTAAATATTGTTATGAATACGGAATTGAACTGTAAAA
* * * *
55840310 TTACTGAATATTGTTATGTATACTGTATTGAACTGTAAAA
1 TTACTAAATATTGTTATGAATACGGAATTGAACTGTAAAA
55840350 TT
1 TT
55840352 TCTGATGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (40 bp):
TTACTAAATATTGTTATGAATACGGAATTGAACTGTAAAA
Found at i:55840637 original size:18 final size:19
Alignment explanation
Indices: 55840610--55840650 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
55840600 GTGTGTCGAA
* *
55840610 TACTGTTACCGTTACT-AT
1 TACTGCTACCGTCACTGAT
55840628 TACTGCTACCGTCACTGAT
1 TACTGCTACCGTCACTGAT
55840647 TACT
1 TACT
55840651 ATTTAGGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (19 bp):
TACTGCTACCGTCACTGAT
Found at i:55856392 original size:21 final size:20
Alignment explanation
Indices: 55856368--55856408 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55856358 ACAAATACGA
55856368 ATGCAAATAAAAATGAAAAAT
1 ATGCAAATAAAAA-GAAAAAT
* *
55856389 ATGCAATTGAAAAGAAAAAT
1 ATGCAAATAAAAAGAAAAAT
55856409 CAAAAGCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (20 bp):
ATGCAAATAAAAAGAAAAAT
Found at i:55858661 original size:5 final size:5
Alignment explanation
Indices: 55858645--55858687 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
55858635 TAGGAAGATA
*
55858645 TTATT TTGTT TTATT TTATTAT TTATT ATTATT TTATT TTATT
1 TTATT TTATT TTATT TTA-T-T TTATT -TTATT TTATT TTATT
55858688 AATTTAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 22 0.67
6 7 0.21
7 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:55862525 original size:47 final size:47
Alignment explanation
Indices: 55862462--55862615 Score: 245
Period size: 47 Copynumber: 3.3 Consensus size: 47
55862452 CCCTTCGGGA
*
55862462 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* * * *
55862509 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
55862556 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
55862603 CTTATCACATATA
1 CTTATCACATATA
55862616 CATATCTTGT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:55870175 original size:20 final size:20
Alignment explanation
Indices: 55870134--55870175 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55870124 ATTTTGTACG
*
55870134 TTGGCCCATTTTCTCTTTTT
1 TTGGCCCATTTTCTCTTCTT
55870154 TTGGCCCA-TTTCTCGTTCTT
1 TTGGCCCATTTTCTC-TTCTT
55870174 TT
1 TT
55870176 CACTCTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.05, C:0.26, G:0.12, T:0.57
Consensus pattern (20 bp):
TTGGCCCATTTTCTCTTCTT
Found at i:55870435 original size:47 final size:47
Alignment explanation
Indices: 55870363--55870457 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
55870353 TAACGACGTT
* *
55870363 AAAAAGCGCTTTTTGGGAGGTAACCCAAATTTATTTTCATTTATTTA
1 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
55870410 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
1 AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
55870457 A
1 A
55870458 TTTTTAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (47 bp):
AAAAAGCGCTTTTTGGAAGGCAACCCAAATTTATTTTCATTTATTTA
Found at i:55872065 original size:21 final size:21
Alignment explanation
Indices: 55872041--55872085 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55872031 CCACTCTTGA
55872041 TATG-TTAAATATTCATGATGC
1 TATGATTAAATATT-ATGATGC
* *
55872062 TATGATTAATTATTTTGATGC
1 TATGATTAAATATTATGATGC
55872083 TAT
1 TAT
55872086 TGGTTGGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (21 bp):
TATGATTAAATATTATGATGC
Found at i:55873335 original size:4 final size:4
Alignment explanation
Indices: 55873326--55873366 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
55873316 TTTCTTGTGC
* *
55873326 ATAA ATAA ATAC ATAA ATAA ATAC ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
55873367 GGTTCAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:55873342 original size:12 final size:12
Alignment explanation
Indices: 55873325--55873366 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
55873315 TTTTCTTGTG
55873325 CATAAATAAATA
1 CATAAATAAATA
55873337 CATAAATAAATA
1 CATAAATAAATA
55873349 CATAAATAAATA
1 CATAAATAAATA
*
55873361 AATAAA
1 CATAAA
55873367 GGTTCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
CATAAATAAATA
Found at i:55874150 original size:12 final size:13
Alignment explanation
Indices: 55874133--55874161 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55874123 ATTATTTTGT
55874133 TTTATTTTATT-A
1 TTTATTTTATTAA
55874145 TTTATTTTATTAA
1 TTTATTTTATTAA
55874158 TTTA
1 TTTA
55874162 GGTTAGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTATTAA
Found at i:55879614 original size:20 final size:20
Alignment explanation
Indices: 55879582--55879656 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
55879572 ATACGTGGGT
55879582 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
*
55879599 ATATGATATGTACATGATATG
1 -TATGATATGCACATGATATG
55879620 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
55879640 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
55879657 GAATTCATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 8 0.15
20 42 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:55879617 original size:11 final size:11
Alignment explanation
Indices: 55879589--55879641 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
55879579 GGTTATGATA
55879589 TACATGAT-TG
1 TACATGATATG
*
55879599 -ATATGATATG
1 TACATGATATG
55879609 TACATGATATG
1 TACATGATATG
55879620 T--ATGATATG
1 TACATGATATG
*
55879629 CACATGATATG
1 TACATGATATG
55879640 TA
1 TA
55879642 TGAAATGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
TACATGATATG
Found at i:55879735 original size:26 final size:26
Alignment explanation
Indices: 55879706--55879803 Score: 162
Period size: 26 Copynumber: 3.8 Consensus size: 26
55879696 GAGGAAGTGC
55879706 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
55879732 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
55879758 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
55879784 AAAAGGGCTT-CGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
55879804 ATTAAAGAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 9 0.13
26 60 0.87
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:55880865 original size:67 final size:67
Alignment explanation
Indices: 55880739--55880865 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 67
55880729 CCAGTTGCAA
***
55880739 CAACTCGGCTGTGGATCGGGTTCGAAAAACTTTTCGAAAAAATGTTACATTTAGTGGTATCAGAG
1 CAACTCGGCTGTGGATCGGGTTCGAAAAACTTTTCGAAAAAATGTTACAAGAAGTGGTATCAGAG
55880804 CC
66 CC
55880806 CAACTCGGCTGTGGATCGGGTTCGAAAAACTTTTCGAAAAAAAT-TTACCAAGAAG-GGTAT
1 CAACTCGGCTGTGGATCGGGTTCGAAAAACTTTTCG-AAAAAATGTTA-CAAGAAGTGGTAT
55880866 TTTTTGGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
67 44 0.80
68 11 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (67 bp):
CAACTCGGCTGTGGATCGGGTTCGAAAAACTTTTCGAAAAAATGTTACAAGAAGTGGTATCAGAG
CC
Found at i:55887697 original size:9 final size:10
Alignment explanation
Indices: 55887685--55887741 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
55887675 TACGTGGGAT
55887685 ATGATAT-AC
1 ATGATATGAC
*
55887694 ATGAT-TGAT
1 ATGATATGAC
55887703 ATGATATGCAC
1 ATGATATG-AC
*
55887714 ATGATATG-T
1 ATGATATGAC
55887723 ATGATATGCAC
1 ATGATATG-AC
55887734 ATGATATG
1 ATGATATG
55887742 TATGAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:55887717 original size:20 final size:20
Alignment explanation
Indices: 55887684--55887758 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
55887674 ATACGTGGGA
55887684 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
55887701 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
55887722 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
55887742 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
55887759 GAATTCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:55887719 original size:11 final size:11
Alignment explanation
Indices: 55887703--55887758 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
55887693 CATGATTGAT
55887703 ATGATATGCAC
1 ATGATATGCAC
*
55887714 ATGATATG--T
1 ATGATATGCAC
55887723 ATGATATGCAC
1 ATGATATGCAC
*
55887734 ATGATATG--T
1 ATGATATGCAC
*
55887743 ATGAAATGCAC
1 ATGATATGCAC
55887754 ATGAT
1 ATGAT
55887759 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:55887837 original size:26 final size:26
Alignment explanation
Indices: 55887808--55887879 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
55887798 GAGGAAGTGC
*
55887808 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
55887834 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
55887860 AAAAGGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
55887880 ATTAAAGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 9 0.20
26 35 0.80
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:55888987 original size:13 final size:13
Alignment explanation
Indices: 55888969--55889001 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
55888959 CTGTGTCTCT
55888969 CACACGGTCGAGA
1 CACACGGTCGAGA
55888982 CACACGGTCGAGA
1 CACACGGTCGAGA
55888995 CACACGG
1 CACACGG
55889002 CCGTGTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.30, T:0.06
Consensus pattern (13 bp):
CACACGGTCGAGA
Found at i:55890100 original size:42 final size:43
Alignment explanation
Indices: 55889978--55890186 Score: 126
Period size: 42 Copynumber: 4.9 Consensus size: 43
55889968 AGTAAGATGC
* * * ** * *
55889978 CAATGCCATATCCTAGATATGCTCTTACATGGGA-TCACATAT
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
* * *
55890020 CAAAGCCAATAGCCCA-ACTATGGTC--ATACACGATGTCTCATAT
1 CAATGCC-ATATCCCAGA-TATGGTCTTATACA-GAAGTCTCATAT
* * *
55890063 CGATGTCATATCCCAGATATGGTCTTATA-AGAAGTCTCATTTT
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCA-TAT
* * * * * * * **
55890106 TAAAGCCATGTCCCAAACATGGTCTTATACA-AAATCACATGC
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
*
55890148 CTATGCCATATCCCAGATATGGTCTTATACAGAA-TCTCA
1 CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCA
55890187 ATAACCCTAA
Statistics
Matches: 123, Mismatches: 34, Indels: 20
0.69 0.19 0.11
Matches are distributed among these distances:
41 2 0.02
42 60 0.49
43 57 0.46
44 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (43 bp):
CAATGCCATATCCCAGATATGGTCTTATACAGAAGTCTCATAT
Found at i:55919651 original size:40 final size:40
Alignment explanation
Indices: 55919592--55919939 Score: 606
Period size: 40 Copynumber: 8.7 Consensus size: 40
55919582 GAGCATTGGA
*
55919592 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
55919632 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
55919672 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
55919712 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
55919752 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
55919792 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
55919832 ATATATCCGGACTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
55919872 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
55919912 ATATGTTCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
55919940 ATGTGTTTGC
Statistics
Matches: 294, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 294 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Done.