Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 68 of 135
Found at i:27154373 original size:22 final size:23
Alignment explanation
Indices: 27154335--27154378 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27154325 AAATATGAAC
27154335 TAATTGAATTTTAATTAATTTTA
1 TAATTGAATTTTAATTAATTTTA
*
27154358 TAATT-AATTTTGATTAATTTT
1 TAATTGAATTTTAATTAATTTT
27154379 GGTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TAATTGAATTTTAATTAATTTTA
Found at i:27154379 original size:10 final size:10
Alignment explanation
Indices: 27154335--27154378 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
27154325 AAATATGAAC
27154335 TAATTGAATTT
1 TAATT-AATTT
27154346 TAATTAATTTT
1 TAATTAA-TTT
27154357 ATAATTAATTT
1 -TAATTAATTT
*
27154368 TGATTAATTT
1 TAATTAATTT
27154378 T
1 T
27154379 GGTTATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 12 0.40
11 11 0.37
12 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
TAATTAATTT
Found at i:27155247 original size:21 final size:20
Alignment explanation
Indices: 27155202--27155247 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
27155192 TTGTTGGAAT
27155202 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
27155221 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
27155242 GGTTGA
1 GGTTGA
27155248 TTGCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:27157039 original size:32 final size:32
Alignment explanation
Indices: 27156995--27157088 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 32
27156985 AGCCATAAGT
* **
27156995 ACAGTAATATGATTGGCACAAAGCCATCATTA
1 ACAGTAATATGATCGGCACAAAGCCATCAGAA
** * *
27157027 GTAGTGATATGATCGGCACACAGCCATCAGAA
1 ACAGTAATATGATCGGCACAAAGCCATCAGAA
*
27157059 ACGGTAATATGATCGGCACAAAGCCATCAG
1 ACAGTAATATGATCGGCACAAAGCCATCAG
27157089 TAGCATCGTA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (32 bp):
ACAGTAATATGATCGGCACAAAGCCATCAGAA
Found at i:27157289 original size:24 final size:24
Alignment explanation
Indices: 27157262--27157343 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
27157252 CCATGCTCAG
*
27157262 AATCAGTTATACAAATAACAGACA
1 AATCAGTCATACAAATAACAGACA
* * *
27157286 AATCAGTCATACCAATTATAGACA
1 AATCAGTCATACAAATAACAGACA
** *
27157310 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATAACAGACA
27157334 AATCAGTCAT
1 AATCAGTCAT
27157344 TTACGTCACG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATAACAGACA
Found at i:27157344 original size:24 final size:24
Alignment explanation
Indices: 27157274--27157370 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
27157264 TCAGTTATAC
* **
27157274 AAATAACAGACAAATCAGTCATAC
1 AAATCACAGACAAATCAGTCATTT
* * *
27157298 CAATTATAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
27157322 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
** * *
27157346 ACGTCACGGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
27157370 A
1 A
27157371 CACTCGTGGG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (24 bp):
AAATCACAGACAAATCAGTCATTT
Found at i:27157446 original size:27 final size:27
Alignment explanation
Indices: 27157409--27157612 Score: 128
Period size: 27 Copynumber: 7.6 Consensus size: 27
27157399 CTCTAGAGGC
* *
27157409 ATTACGGTCATTTTACCTTACAAGGGT
1 ATTACGATCATTTTACCTTATAAGGGT
* * **
27157436 ATTTCGATCA-TTTAGCCCTATGGGGGT
1 ATTACGATCATTTTA-CCTTATAAGGGT
* *
27157463 ATTACGGTCATTTTACCTTATAAGGGC
1 ATTACGATCATTTTACCTTATAAGGGT
* * * *
27157490 ATTACGATCATTTTATCATAT-GGGGAC
1 ATTACGATCATTTTACCTTATAAGGG-T
* *
27157517 ATTACGGTCA-TTTACCCTATAAGGGT
1 ATTACGATCATTTTACCTTATAAGGGT
* * * * *
27157543 TTTTCGGTCATTTTACCCTA-CAGAGGT
1 ATTACGATCATTTTACCTTATAAG-GGT
* * * *
27157570 ATTACGGTCATTTTACCCTATAGGGGC
1 ATTACGATCATTTTACCTTATAAGGGT
* *
27157597 ATTACGGTTATTTTAC
1 ATTACGATCATTTTAC
27157613 AAATATTGAG
Statistics
Matches: 140, Mismatches: 30, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
26 25 0.18
27 110 0.79
28 5 0.04
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (27 bp):
ATTACGATCATTTTACCTTATAAGGGT
Found at i:27157474 original size:54 final size:54
Alignment explanation
Indices: 27157409--27157591 Score: 217
Period size: 54 Copynumber: 3.4 Consensus size: 54
27157399 CTCTAGAGGC
*
27157409 ATTACGGTCATTTTACCTTACAAGGGTATTTCGATCA-TTTAGCCCTATGGGGGT
1 ATTACGGTCATTTTACCTTATAAGGGTATTTCGATCATTTTA-CCCTATGGGGGT
* * * * **
27157463 ATTACGGTCATTTTACCTTATAAGGGCATTACGATCATTTTATCATATGGGGAC
1 ATTACGGTCATTTTACCTTATAAGGGTATTTCGATCATTTTACCCTATGGGGGT
* * * ** *
27157517 ATTACGGTCA-TTTACCCTATAAGGGTTTTTCGGTCATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCTTATAAGGGTATTTCGATCATTTTACCCTATGGGGGT
*
27157570 ATTACGGTCATTTTACCCTATA
1 ATTACGGTCATTTTACCTTATA
27157592 GGGGCATTAC
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
53 41 0.38
54 63 0.58
55 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (54 bp):
ATTACGGTCATTTTACCTTATAAGGGTATTTCGATCATTTTACCCTATGGGGGT
Found at i:27157531 original size:107 final size:108
Alignment explanation
Indices: 27157408--27157611 Score: 286
Period size: 107 Copynumber: 1.9 Consensus size: 108
27157398 CCTCTAGAGG
* ** *
27157408 CATTACGGTCATTTTACCTTACAAGGGTATTTCGATCA-TTTAGCCCTATGGGGGTATTACGGTC
1 CATTACGGTCATTTTACCCTACAAGGGTATTTCGATCATTTTA-CCCTACAGAGGTATTACGGTC
*
27157472 ATTTTACCTTATAAGGGCATTACGATCATTTTATCATATGGGGA
65 ATTTTACCCTATAAGGGCATTACGATCATTTTATCATATGGGGA
* * *
27157516 CATTACGGTCA-TTTACCCTATAAGGGTTTTTCGGTCATTTTACCCTACAGAGGTATTACGGTCA
1 CATTACGGTCATTTTACCCTACAAGGGTATTTCGATCATTTTACCCTACAGAGGTATTACGGTCA
* * *
27157580 TTTTACCCTATAGGGGCATTACGGTTATTTTA
66 TTTTACCCTATAAGGGCATTACGATCATTTTA
27157612 CAAATATTGA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 69 0.82
108 15 0.18
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (108 bp):
CATTACGGTCATTTTACCCTACAAGGGTATTTCGATCATTTTACCCTACAGAGGTATTACGGTCA
TTTTACCCTATAAGGGCATTACGATCATTTTATCATATGGGGA
Found at i:27157574 original size:80 final size:81
Alignment explanation
Indices: 27157389--27157609 Score: 209
Period size: 80 Copynumber: 2.8 Consensus size: 81
27157379 GGGCAAAATA
* * * * * * * *
27157389 GTCA-TTTACCCT-CTAGAGGCATTACGGTCATTTTACCTTACAAGGGTATTTCGATCATTTAGC
1 GTCATTTTACCCTACAAG-GGCATTACGATCATTTTACCATATAGGGGCATTACGGTCATTTAGC
**
27157452 CCTATGGGGGTATTACG
65 CCTATAAGGGTATTACG
* * *
27157469 GTCATTTTACCTTATAAGGGCATTACGATCATTTTATCATAT-GGGGACATTACGGTCATTTA-C
1 GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCATATAGGGG-CATTACGGTCATTTAGC
* *
27157532 CCTATAAGGGTTTTTCG
65 CCTATAAGGGTATTACG
* * * *
27157549 GTCATTTTACCCTAC-AGAGGTATTACGGTCATTTTACCCTATAGGGGCATTACGGTTATTT
1 GTCATTTTACCCTACAAG-GGCATTACGATCATTTTACCATATAGGGGCATTACGGTCATTT
27157610 TACAAATATT
Statistics
Matches: 114, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
79 2 0.02
80 67 0.59
81 43 0.38
82 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (81 bp):
GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCATATAGGGGCATTACGGTCATTTAGCC
CTATAAGGGTATTACG
Found at i:27157610 original size:54 final size:54
Alignment explanation
Indices: 27157393--27157612 Score: 196
Period size: 54 Copynumber: 4.1 Consensus size: 54
27157383 AAAATAGTCA
* * * *
27157393 TTTACCCT-CTAGAGGCATTACGGTCATTTTACCTTACAAGGGTATTTCGATCA-
1 TTTACCCTAC-AGAGGCATTACGGTCATTTTACCCTATAAGGGCATTACGATCAT
** * * *
27157446 TTTAGCCCTATGGGGGTATTACGGTCATTTTACCTTATAAGGGCATTACGATCAT
1 TTTA-CCCTACAGAGGCATTACGGTCATTTTACCCTATAAGGGCATTACGATCAT
* * * * ** * *
27157501 TTTATCATA-TGGGGACATTACGGTCA-TTTACCCTATAAGGGTTTTTCGGTCAT
1 TTTACCCTACAGAGG-CATTACGGTCATTTTACCCTATAAGGGCATTACGATCAT
* * * *
27157554 TTTACCCTACAGAGGTATTACGGTCATTTTACCCTATAGGGGCATTACGGTTAT
1 TTTACCCTACAGAGGCATTACGGTCATTTTACCCTATAAGGGCATTACGATCAT
27157608 TTTAC
1 TTTAC
27157613 AAATATTGAG
Statistics
Matches: 135, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
53 47 0.35
54 84 0.62
55 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (54 bp):
TTTACCCTACAGAGGCATTACGGTCATTTTACCCTATAAGGGCATTACGATCAT
Found at i:27164619 original size:12 final size:12
Alignment explanation
Indices: 27164602--27164626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27164592 AAGACTGGAT
27164602 GATGCTTTATGG
1 GATGCTTTATGG
27164614 GATGCTTTATGG
1 GATGCTTTATGG
27164626 G
1 G
27164627 CTTACAGGAT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GATGCTTTATGG
Found at i:27189087 original size:13 final size:13
Alignment explanation
Indices: 27189066--27189100 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
27189056 ATAAGTTGCT
* *
27189066 GTTAGTTAAATTA
1 GTTAATTAAATAA
27189079 GTTAATTAAATAA
1 GTTAATTAAATAA
27189092 GTTAATTAA
1 GTTAATTAA
27189101 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:27192806 original size:14 final size:16
Alignment explanation
Indices: 27192789--27192820 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
27192779 AATTAATATT
27192789 AAAACAT-TAT-TAAA
1 AAAACATATATATAAA
27192803 AAAACATATATATAAA
1 AAAACATATATATAAA
27192819 AA
1 AA
27192821 TAACTACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAACATATATATAAA
Found at i:27193373 original size:22 final size:22
Alignment explanation
Indices: 27193345--27193388 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27193335 TCGAGTGACT
*
27193345 TTACACAAAACTAATGAGAGCA
1 TTACACAAAACTAATAAGAGCA
27193367 TTACACAAAACTAATAAGAGCA
1 TTACACAAAACTAATAAGAGCA
27193389 AGGATGGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (22 bp):
TTACACAAAACTAATAAGAGCA
Found at i:27208419 original size:5 final size:5
Alignment explanation
Indices: 27208409--27208440 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
27208399 TCATATATGC
27208409 TTTTA TTTTA --TTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
27208441 TTCCCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:27208427 original size:13 final size:13
Alignment explanation
Indices: 27208409--27208433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27208399 TCATATATGC
27208409 TTTTATTTTATTA
1 TTTTATTTTATTA
27208422 TTTTATTTTATT
1 TTTTATTTTATT
27208434 TTATTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:27208430 original size:18 final size:17
Alignment explanation
Indices: 27208409--27208442 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
27208399 TCATATATGC
27208409 TTTTATTTTATTATTTTA
1 TTTTATTTTATT-TTTTA
27208427 TTTTATTTTATTTTTT
1 TTTTATTTTATTTTTT
27208443 CCCAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTATTTTTTA
Found at i:27217613 original size:2 final size:2
Alignment explanation
Indices: 27217606--27217643 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
27217596 NNNNTCTTTA
27217606 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27217644 TTTGTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27223970 original size:16 final size:16
Alignment explanation
Indices: 27223949--27224000 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
27223939 TTTGGTTCGC
27223949 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27223965 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
27223981 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
27223997 TGTA
1 TGTA
27224001 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:27227531 original size:19 final size:20
Alignment explanation
Indices: 27227473--27227533 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
27227463 GAAGATAATA
* *
27227473 AAAAATATAAAA--ATTATG
1 AAAAATAGAAAATTATTATT
*
27227491 AAAAATAGAAAATTTTTATT
1 AAAAATAGAAAATTATTATT
27227511 AAAAATAGAAAGA-TATT-TT
1 AAAAATAGAAA-ATTATTATT
27227530 AAAA
1 AAAA
27227534 TCATAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.31
19 6 0.17
20 18 0.50
21 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATAGAAAATTATTATT
Found at i:27227602 original size:20 final size:19
Alignment explanation
Indices: 27227574--27227626 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
27227564 AAAATATTAT
27227574 AAAATATAAAA-ATATAGAA
1 AAAATATAAAATATATA-AA
27227593 AAAATGATAAAGATATATAAA
1 AAAAT-ATAAA-ATATATAAA
27227614 AAAATCATAAAAT
1 AAAAT-ATAAAAT
27227627 GTGTTCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
21 13 0.43
22 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAATATAAAATATATAAA
Found at i:27227625 original size:11 final size:10
Alignment explanation
Indices: 27227560--27227625 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
27227550 AAATTATTTT
27227560 TAAAAAAATA
1 TAAAAAAATA
* *
27227570 TTATAAAATA
1 TAAAAAAATA
27227580 T--AAAAATA
1 TAAAAAAATA
27227588 TAGAAAAAATGA
1 TA-AAAAAAT-A
* *
27227600 TAAAGATATA
1 TAAAAAAATA
27227610 TAAAAAAATCA
1 TAAAAAAAT-A
27227621 TAAAA
1 TAAAA
27227626 TGTGTTCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.16
10 17 0.39
11 17 0.39
12 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.24
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:27228265 original size:58 final size:59
Alignment explanation
Indices: 27228170--27228281 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
27228160 AATTTTAAGC
27228170 TTTAAATATTTTATATTTAATAATATTTTTAATATTTT-TTTCTAAAATTTTAATTAAA
1 TTTAAATATTTTATATTTAATAATATTTTTAATATTTTCTTTCTAAAATTTTAATTAAA
* * * *
27228228 TTTAATTATTTTTATATTT-TTCAATATTTTT-ATATTTTCTTTCTATATTTTTAA
1 TTTAAATA-TTTTATATTTAAT-AATATTTTTAATATTTTCTTTCTAAAATTTTAA
27228282 CGTTTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 15 0.32
59 32 0.68
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (59 bp):
TTTAAATATTTTATATTTAATAATATTTTTAATATTTTCTTTCTAAAATTTTAATTAAA
Found at i:27228901 original size:10 final size:9
Alignment explanation
Indices: 27228881--27228936 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
27228871 AACCAATTAG
*
27228881 TATACAAAA
1 TATATAAAA
27228890 TATTATAAAA
1 TA-TATAAAA
27228900 TATA-AAAA
1 TATATAAAA
*
27228908 TATAGAAAA
1 TATATAAAA
*
27228917 AATGATAAAGA
1 TAT-ATAAA-A
27228928 TATATAAAA
1 TATATAAAA
27228937 AAATCATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 8 0.21
9 11 0.28
10 17 0.44
11 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (9 bp):
TATATAAAA
Found at i:27228930 original size:20 final size:19
Alignment explanation
Indices: 27228896--27228947 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
27228886 AAAATATTAT
27228896 AAAATATAAAAATATAGAA
1 AAAATATAAAAATATAGAA
27228915 AAAATGATAAAGATATATA-AA
1 AAAAT-ATAAA-A-ATATAGAA
27228936 AAAATCATAAAA
1 AAAAT-ATAAAA
27228948 TGTGTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 6 0.21
21 13 0.45
22 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAATATAAAAATATAGAA
Found at i:27229096 original size:18 final size:16
Alignment explanation
Indices: 27229045--27229096 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
27229035 GAGGAGAATG
27229045 ATAAA-AAAAATTAAA
1 ATAAATAAAAATTAAA
*
27229060 ATCAATAAAAATATAAAA
1 ATAAATAAAAAT-T-AAA
27229078 ATAAATAAACAATTGAAA
1 ATAAATAAA-AATT-AAA
27229096 A
1 A
27229097 GTCTAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.13
16 6 0.20
17 1 0.03
18 16 0.53
19 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (16 bp):
ATAAATAAAAATTAAA
Found at i:27230031 original size:58 final size:59
Alignment explanation
Indices: 27229936--27230047 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
27229926 AATTTTAAGC
27229936 TTTAAATATTTTATATTTAATAATATTTTTAATATTTT-TTTCTAAAATTTTAATTAAA
1 TTTAAATATTTTATATTTAATAATATTTTTAATATTTTCTTTCTAAAATTTTAATTAAA
* * * *
27229994 TTTAATTATTTTTATATTT-TTCAATATTTTT-ATATTTTCTTTCTATATTTTTAA
1 TTTAAATA-TTTTATATTTAAT-AATATTTTTAATATTTTCTTTCTAAAATTTTAA
27230048 CGTTTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 15 0.32
59 32 0.68
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (59 bp):
TTTAAATATTTTATATTTAATAATATTTTTAATATTTTCTTTCTAAAATTTTAATTAAA
Found at i:27243983 original size:3 final size:3
Alignment explanation
Indices: 27243975--27244015 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
27243965 AGTTGGAAGA
27243975 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
27244016 AAACTTCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:27244024 original size:15 final size:15
Alignment explanation
Indices: 27243975--27244033 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
27243965 AGTTGGAAGA
* *
27243975 ATCATCATCATCATC
1 ATCATCATCATAAAC
* *
27243990 ATCATCATCATCATC
1 ATCATCATCATAAAC
27244005 ATCATCATCATAAAC
1 ATCATCATCATAAAC
* *
27244020 TTCATCTTCATAAA
1 ATCATCATCATAAA
27244034 TGGTTTCTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCATCATCATAAAC
Found at i:27252162 original size:15 final size:15
Alignment explanation
Indices: 27252144--27252174 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27252134 GCATGGAATT
*
27252144 CCACGGTTTGTAGAA
1 CCACGATTTGTAGAA
27252159 CCACGATTTGTAGAA
1 CCACGATTTGTAGAA
27252174 C
1 C
27252175 AAATGTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (15 bp):
CCACGATTTGTAGAA
Found at i:27255918 original size:16 final size:17
Alignment explanation
Indices: 27255885--27255922 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
27255875 AAAAATTATA
* *
27255885 AAAAACTGAATAATATT
1 AAAAACTGAAAAAAATT
27255902 AAAAACT-AAAAAAATT
1 AAAAACTGAAAAAAATT
27255918 AAAAA
1 AAAAA
27255923 TAACTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAACTGAAAAAAATT
Found at i:27257605 original size:30 final size:30
Alignment explanation
Indices: 27257566--27257634 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
27257556 GCTGACACAT
* *
27257566 GGTCATGTGTCACACACGAGCATGTGATAC
1 GGTCGTGTGTCACACACGAGCATGTGACAC
*
27257596 GGTCGTGTGTCACACACGGGCATGTGACAC
1 GGTCGTGTGTCACACACGAGCATGTGACAC
*
27257626 GATCGTGTG
1 GGTCGTGTG
27257635 CTCTTTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (30 bp):
GGTCGTGTGTCACACACGAGCATGTGACAC
Found at i:27262998 original size:19 final size:19
Alignment explanation
Indices: 27262974--27263011 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27262964 CTAATTATAG
27262974 CTGAATAGCTTGAAGTTGA
1 CTGAATAGCTTGAAGTTGA
27262993 CTGAATAGCTTGAAGTTGA
1 CTGAATAGCTTGAAGTTGA
27263012 AAAGAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
CTGAATAGCTTGAAGTTGA
Found at i:27273730 original size:52 final size:52
Alignment explanation
Indices: 27273661--27273766 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
27273651 ACATGGATGG
27273661 TCCCTTTGTTGCTGAGAATGAGATGCAGAATGTCCAAAATATGAACATAGAA
1 TCCCTTTGTTGCTGAGAATGAGATGCAGAATGTCCAAAATATGAACATAGAA
*
27273713 TCCCTTTGTTGCTGAGAATGAGATGCTGAATGTCCAAAATATGAACATAGAA
1 TCCCTTTGTTGCTGAGAATGAGATGCAGAATGTCCAAAATATGAACATAGAA
27273765 TC
1 TC
27273767 AAGTCCAACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (52 bp):
TCCCTTTGTTGCTGAGAATGAGATGCAGAATGTCCAAAATATGAACATAGAA
Found at i:27280445 original size:48 final size:48
Alignment explanation
Indices: 27280382--27280551 Score: 205
Period size: 48 Copynumber: 3.5 Consensus size: 48
27280372 GGTCGCATAT
* *
27280382 GTGGCGCGGGCTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
*
27280430 GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* * * * * ** * **
27280478 GTGGCACAGACTATGCGCAGGCCACCAAGAGTCTGTTATTACACAAAT
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* *
27280526 GTGGTACGGACTGTGTGTAGGCCACC
1 GTGGCACGGACTGTGTGCAGGCCACC
27280552 GAGAAATTTA
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 103 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (48 bp):
GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
Found at i:27283010 original size:8 final size:9
Alignment explanation
Indices: 27282928--27283008 Score: 65
Period size: 10 Copynumber: 8.4 Consensus size: 9
27282918 TTTAATATTT
27282928 TTTTTAAAA
1 TTTTTAAAA
*
27282937 -TTTTAATGA
1 TTTTTAA-AA
*
27282946 TTATTTATAA
1 TT-TTTAAAA
*
27282956 TTATTTATAA
1 TT-TTTAAAA
*
27282966 TTCTTAATAA
1 TTTTTAA-AA
27282976 TTTTTAAAGAA
1 TTTTT-AA-AA
27282987 TTTTTAAAA
1 TTTTTAAAA
27282996 TTTTTAAAA
1 TTTTTAAAA
27283005 TTTT
1 TTTT
27283009 AATTATTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.10
9 19 0.32
10 22 0.37
11 13 0.22
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:27283016 original size:18 final size:18
Alignment explanation
Indices: 27282952--27283016 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
27282942 ATGATTATTT
*
27282952 ATAATTATTTATAATTCTTA
1 ATAATT-TTTAAAATT-TTA
27282972 ATAATTTTTAAAGAATTTTTA
1 ATAATTTTT-AA-AA-TTTTA
27282993 A-AATTTTTAAAATTTTA
1 ATAATTTTTAAAATTTTA
*
27283010 ATTATTT
1 ATAATTT
27283017 GAAAAACCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 5 0.13
20 14 0.36
21 6 0.15
22 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATAATTTTTAAAATTTTA
Found at i:27285288 original size:16 final size:16
Alignment explanation
Indices: 27285267--27285298 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27285257 GAAATTAAAG
*
27285267 AAAAATATTATAGAAT
1 AAAAATATTAAAGAAT
27285283 AAAAATATTAAAGAAT
1 AAAAATATTAAAGAAT
27285299 GTATATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAAATATTAAAGAAT
Found at i:27286131 original size:23 final size:23
Alignment explanation
Indices: 27286101--27286169 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 23
27286091 ATACATCATC
*
27286101 CTCTTTTTTGTTCTTTTTTTTTT
1 CTCTTTTTTGTTCTTTTTCTTTT
27286124 CTCTTTTTTCTGTTTTCTGTTTTCTTTT
1 CTC-TTTTT-TG--TTCT-TTTTCTTTT
*
27286152 CTTCCTTTTTGTTCTTTT
1 C-TCTTTTTTGTTCTTTT
27286170 ATGTGCTGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
23 3 0.08
24 8 0.21
25 6 0.16
27 6 0.16
28 13 0.34
29 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (23 bp):
CTCTTTTTTGTTCTTTTTCTTTT
Found at i:27291867 original size:33 final size:33
Alignment explanation
Indices: 27291842--27291940 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
27291832 ATCACATTGG
*
27291842 TCCTCATAATAGCTAATCCAACCATCACACCAA
1 TCCTCATAAGAGCTAATCCAACCATCACACCAA
* *
27291875 TGCTCATAAGAGCTAAACCAACCATCACACCAA
1 TCCTCATAAGAGCTAATCCAACCATCACACCAA
* * *
27291908 TGCTCATAAGAGCTAATCTAACCAGCACACCAA
1 TCCTCATAAGAGCTAATCCAACCATCACACCAA
27291941 CTAGAGAGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.18
Consensus pattern (33 bp):
TCCTCATAAGAGCTAATCCAACCATCACACCAA
Found at i:27291900 original size:66 final size:66
Alignment explanation
Indices: 27291790--27291940 Score: 151
Period size: 66 Copynumber: 2.3 Consensus size: 66
27291780 ACATCATTAG
* * * **** *
27291790 TCCAACCAAACACACCAGATGCTCAATCGAGCCAATCCATCCATCACATTGGTCCTCATAATAGC
1 TCCAACC-AACACACCA-ATGCTCAATAGAGCCAAACCAACCATCACACCAATCCTCATAAGAGC
27291855 TAA
64 TAA
* * *
27291858 TCCAACCATCACACCAATGCTC-ATAAGAGCTAAACCAACCATCACACCAATGCTCATAAGAGCT
1 TCCAACCAACACACCAATGCTCAAT-AGAGCCAAACCAACCATCACACCAATCCTCATAAGAGCT
27291922 AA
65 AA
* *
27291924 TCTAACCAGCACACCAA
1 TCCAACCAACACACCAA
27291941 CTAGAGAGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
65 2 0.03
66 52 0.75
67 8 0.12
68 7 0.10
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.18
Consensus pattern (66 bp):
TCCAACCAACACACCAATGCTCAATAGAGCCAAACCAACCATCACACCAATCCTCATAAGAGCTA
A
Found at i:27299913 original size:96 final size:96
Alignment explanation
Indices: 27299796--27299985 Score: 281
Period size: 96 Copynumber: 2.0 Consensus size: 96
27299786 AAATAATAAA
* *
27299796 CTCAAAGCAAACATAACTAAAATAAATAACAAGAGGAAAAAGTAAAATCTATTCAGTTGAACAGC
1 CTCAAAGAAAACATAACTAAAATAAATAACAAGAGGAAAAAGTAAAATCTATTCAATTGAACAGC
**
27299861 CTTTTGGATCTATTCTGACTGATGCGCTCCT
66 CTTTCAGATCTATTCTGACTGATGCGCTCCT
* * * * * **
27299892 CTCAAAGAAAACGTAATTAAAATAAATAACAAGAGGAAAGAGTAAACTCTATTCAATTTAGTAGC
1 CTCAAAGAAAACATAACTAAAATAAATAACAAGAGGAAAAAGTAAAATCTATTCAATTGAACAGC
27299957 CTTTCAGATCTATTCTGACTGATGCGCTC
66 CTTTCAGATCTATTCTGACTGATGCGCTC
27299986 TTCTGTTCTG
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (96 bp):
CTCAAAGAAAACATAACTAAAATAAATAACAAGAGGAAAAAGTAAAATCTATTCAATTGAACAGC
CTTTCAGATCTATTCTGACTGATGCGCTCCT
Found at i:27302023 original size:24 final size:24
Alignment explanation
Indices: 27301996--27302059 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
27301986 TAAGTTTCCA
* *
27301996 AAAATGTAAATTGAAATGAAAACT-
1 AAAATGAAAATGGAAATGAAAA-TG
*
27302020 AAAATGGAAATGGAAATGAAAATG
1 AAAATGAAAATGGAAATGAAAATG
27302044 AAAATGAAAATGGAAA
1 AAAATGAAAATGGAAA
27302060 CTTGCAATCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.61, C:0.02, G:0.19, T:0.19
Consensus pattern (24 bp):
AAAATGAAAATGGAAATGAAAATG
Found at i:27302053 original size:6 final size:6
Alignment explanation
Indices: 27301996--27302055 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
27301986 TAAGTTTCCA
* * *
27301996 AAAATG TAAATTG -AAATG AAAACT- AAAATG GAAATG GAAATG AAAATG
1 AAAATG -AAAATG AAAATG AAAA-TG AAAATG AAAATG AAAATG AAAATG
27302044 AAAATG AAAATG
1 AAAATG AAAATG
27302056 GAAACTTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 5 0.11
6 35 0.76
7 6 0.13
ACGTcount: A:0.60, C:0.02, G:0.18, T:0.20
Consensus pattern (6 bp):
AAAATG
Found at i:27309086 original size:36 final size:36
Alignment explanation
Indices: 27309037--27309110 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
27309027 TCGACGACTT
27309037 TTGAGATATTATTATTCTACCGAAAAATAGAGAGAA
1 TTGAGATATTATTATTCTACCGAAAAATAGAGAGAA
* *
27309073 TTGATATATTATTATTCTGCCGAAAAATAGAGAGAA
1 TTGAGATATTATTATTCTACCGAAAAATAGAGAGAA
27309109 TT
1 TT
27309111 TATTCTCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (36 bp):
TTGAGATATTATTATTCTACCGAAAAATAGAGAGAA
Found at i:27314420 original size:25 final size:25
Alignment explanation
Indices: 27314392--27314456 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
27314382 TGATTTACAA
* *
27314392 CTCGTATAAGCTTCCCAATTCATAG
1 CTCGTATAAGCATACCAATTCATAG
* *
27314417 CTCGTGA-GAGCATACTAATTCATAG
1 CTCGT-ATAAGCATACCAATTCATAG
*
27314442 CTCGTATGAGCATAC
1 CTCGTATAAGCATAC
27314457 ATGAATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (25 bp):
CTCGTATAAGCATACCAATTCATAG
Found at i:27322617 original size:5 final size:5
Alignment explanation
Indices: 27322607--27322633 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
27322597 GGTCCATGCT
27322607 AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AA
27322634 CAACTTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:27324906 original size:306 final size:309
Alignment explanation
Indices: 27324506--27325076 Score: 731
Period size: 306 Copynumber: 1.9 Consensus size: 309
27324496 TACACGTATA
* * ** *
27324506 ATAGAATTTCTAGTATTAATAATGTTGTTGATTGAATTGGTGTCACAAATTATCTTGACACCAGC
1 ATAGAATTTCTAGTATTAATAATATTGTTGATTGAATTGATGTCACAAATTAAATGGACACCAGC
* * * * * * *
27324571 TTAGGATTACTGGCAACACCATGATAAACAATTATATTTATTTAGTATTCCTAAT-ACGATGTAT
66 TCAAGATTACTGACAACACCATAATAAACAAATATATTGATTTAGTATTACTAATCA-GATGTAT
* ** * *
27324635 CTATGCGTTTAAATTTTGTTTTACTCACAATTTAATATAA-ACGTTTCATTTTAATATCACACAT
130 CTATGCATTTAAATTTCATTTTACTCACAAGTTAATATAATA-GTTTCATTTTAATATCACACAA
* * * *
27324699 ATTTAATGTGTTATTATTAATTAGTTTTAAACCATATGTTT-A-AATTTATTATATGCTATTTTT
194 ATTCAATGTGTTATTATTAATTAGTTTCAAACCATACGTTTCATAATTTATTATATGCTATTTAT
27324762 AAACACACATTTTTGTTCTAAATATGTGATCTGTAGATGTATCTACATGTG
259 AAACACACATTTTTGTTCTAAATATGTGATCTGTAGATGTATCTACATGTG
*
27324813 ATAGAATTTCTAGTATT-ATAATATTGTTGATTGAGTTGATGTCACAAATTAAATGGACACCAGC
1 ATAGAATTTCTAGTATTAATAATATTGTTGATTGAATTGATGTCACAAATTAAATGGACACCAGC
* * *
27324877 TCAAGATTGA-TGACAGCACCATAATAAACAAATGTATTGATTTAGTATTATTAATCAGATGTAT
66 TCAAGATT-ACTGACAACACCATAATAAACAAATATATTGATTTAGTATTACTAATCAGATGTAT
* * * ** *
27324941 TTATGCATTTAAATTTCATTTTACTCACAAGTTAATCTAATTTATTTTCATTTTAATATCGTATA
130 CTATGCATTTAAATTTCATTTTACTCACAAGTTAATATAA--TAGTTTCATTTTAATATCACACA
* * * * *
27325006 AATTCCATGTGTTATTATTAATTAGTTTCAAATCATACGTTTCATTATTTATTGTATGTTATTTA
193 AATTCAATGTGTTATTATTAATTAGTTTCAAACCATACGTTTCATAATTTATTATATGCTATTTA
27325071 TAAACA
258 TAAACA
27325077 TATCTTTGTA
Statistics
Matches: 221, Mismatches: 36, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
306 125 0.57
307 19 0.09
308 53 0.24
309 2 0.01
310 22 0.10
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (309 bp):
ATAGAATTTCTAGTATTAATAATATTGTTGATTGAATTGATGTCACAAATTAAATGGACACCAGC
TCAAGATTACTGACAACACCATAATAAACAAATATATTGATTTAGTATTACTAATCAGATGTATC
TATGCATTTAAATTTCATTTTACTCACAAGTTAATATAATAGTTTCATTTTAATATCACACAAAT
TCAATGTGTTATTATTAATTAGTTTCAAACCATACGTTTCATAATTTATTATATGCTATTTATAA
ACACACATTTTTGTTCTAAATATGTGATCTGTAGATGTATCTACATGTG
Found at i:27330402 original size:34 final size:34
Alignment explanation
Indices: 27330359--27330427 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
27330349 ATAAATGGGT
27330359 CTGCTCACACAAGCCGGCGGTCGGAATGTAGCTA
1 CTGCTCACACAAGCCGGCGGTCGGAATGTAGCTA
*
27330393 CTGCTCACACAAGCTGGCGGTCGGAATGTAGCTA
1 CTGCTCACACAAGCCGGCGGTCGGAATGTAGCTA
27330427 C
1 C
27330428 AAGATGCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (34 bp):
CTGCTCACACAAGCCGGCGGTCGGAATGTAGCTA
Found at i:27335424 original size:14 final size:14
Alignment explanation
Indices: 27335405--27335450 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
27335395 ACTCAACTTA
27335405 AAATTTAATATTTT
1 AAATTTAATATTTT
*
27335419 AAATTTAATA-GTT
1 AAATTTAATATTTT
27335432 -AATTT-ATAATTTT
1 AAATTTAAT-ATTTT
27335445 AAATTT
1 AAATTT
27335451 TAAAAATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 6 0.22
13 4 0.15
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
AAATTTAATATTTT
Found at i:27336773 original size:16 final size:16
Alignment explanation
Indices: 27336748--27336778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27336738 TTAGTAATAA
*
27336748 ATTTATTTTAAATTTT
1 ATTTAATTTAAATTTT
27336764 ATTTAATTTAAATTT
1 ATTTAATTTAAATTT
27336779 GAATCTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAATTTAAATTTT
Found at i:27337171 original size:75 final size:75
Alignment explanation
Indices: 27337004--27337213 Score: 273
Period size: 75 Copynumber: 2.8 Consensus size: 75
27336994 TGAAATTCAA
** *
27337004 TTTTGATCCCT-TACTATGCTAACATTTGGGATTTAATCCCTTTTAGTCA-TATAAGATGATGAT
1 TTTTGATCCCTCTACTATGCTAACATTTGGGATTTAATCATTTTTAGTCATTATAAGATAATGAT
*
27337067 TAAATTATAG
66 CAAATTATAG
* * *
27337077 TTTTGACCCCTCTACTATGCTCACATTTGGGATTTAATCTTTTTTAGTCATTATAAGATAATGAT
1 TTTTGATCCCTCTACTATGCTAACATTTGGGATTTAATCATTTTTAGTCATTATAAGATAATGAT
*
27337142 CAAATTGTAG
66 CAAATTATAG
* * * * *
27337152 TTTTGGTCCCTCTATTATGCTTAA-ATTTGGAATTTGATCATTTTTAATCATTATAAGATAAT
1 TTTTGATCCCTCTACTATGC-TAACATTTGGGATTTAATCATTTTTAGTCATTATAAGATAAT
27337214 ATGCTCACTT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
73 10 0.08
74 35 0.29
75 72 0.61
76 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (75 bp):
TTTTGATCCCTCTACTATGCTAACATTTGGGATTTAATCATTTTTAGTCATTATAAGATAATGAT
CAAATTATAG
Found at i:27343581 original size:45 final size:45
Alignment explanation
Indices: 27343548--27343660 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
27343538 TGAGATAGTT
* *
27343548 TCTTTCAGCT-ATGGTTTTACTCGATAGAATCGTGATGCCATAACG
1 TCTTTCA-CTCATGGTATTACTCGATAGAATCGTGATGACATAACG
* *
27343593 TCTTTCACTCATGGTATTACTTGATAGAATCGTGATGCCATAACG
1 TCTTTCACTCATGGTATTACTCGATAGAATCGTGATGACATAACG
* *
27343638 TCTTTCAATCATGGTCTTACTCG
1 TCTTTCACTCATGGTATTACTCG
27343661 TTTCTAGTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 2 0.03
45 60 0.97
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (45 bp):
TCTTTCACTCATGGTATTACTCGATAGAATCGTGATGACATAACG
Found at i:27349787 original size:20 final size:20
Alignment explanation
Indices: 27349725--27349778 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
27349715 AAGCTCCATG
* * **
27349725 GTATTGATATTTTTACACGA
1 GTATCGATATTTTTATAAAA
27349745 GTATCGATATTTTTATAAAA
1 GTATCGATATTTTTATAAAA
27349765 GTATCGATATTTTT
1 GTATCGATATTTTT
27349779 TAGTTAGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
GTATCGATATTTTTATAAAA
Found at i:27358133 original size:44 final size:45
Alignment explanation
Indices: 27358083--27358185 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 45
27358073 CTTATTTATT
* *
27358083 CATGGTCTTATTTATTCTT-GTCTTAATGCCAT-GTGTCTTTCAAC
1 CATGGTCTTATTCATT-TTCGTCGTAATGCCATAGTGTCTTTCAAC
** *
27358127 CATGGTCTTATTCATTTTCCGTCGTGTTGCCATAGTGTTTTTCAAC
1 CATGGTCTTATTCATTTT-CGTCGTAATGCCATAGTGTCTTTCAAC
27358173 CATGGTCTTATTC
1 CATGGTCTTATTC
27358186 GTTTGATTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 2 0.04
44 15 0.29
45 10 0.20
46 24 0.47
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.47
Consensus pattern (45 bp):
CATGGTCTTATTCATTTTCGTCGTAATGCCATAGTGTCTTTCAAC
Found at i:27358215 original size:45 final size:45
Alignment explanation
Indices: 27358117--27358319 Score: 158
Period size: 45 Copynumber: 4.5 Consensus size: 45
27358107 AATGCCATGT
**** * **
27358117 GTCTTTCAACCATGGTCTTATTC-ATTTTCCGTCGTGTTGCCATAGT
1 GTCTTTCAACCATGGTCTTATTCGA--TAGAATCGTGATGCCATAAC
* * * * * *
27358163 GTTTTTCAACCATGGTCTTATTCGTTTGATTCGTGATGTCATAGC
1 GTCTTTCAACCATGGTCTTATTCGATAGAATCGTGATGCCATAAC
* * * *
27358208 GTCTTTCAGCTATGGCCTTACTCGATAGAATCGTGATGCCATAAC
1 GTCTTTCAACCATGGTCTTATTCGATAGAATCGTGATGCCATAAC
* * * *
27358253 ATCTTT-AAGTCATGGTCTTACTCGATAGAATCATGATGCCATAAC
1 GTCTTTCAA-CCATGGTCTTATTCGATAGAATCGTGATGCCATAAC
**
27358298 GTCTTTCAGTCATGGTCTTATT
1 GTCTTTCAACCATGGTCTTATT
27358320 TATTCTCCGG
Statistics
Matches: 127, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
44 1 0.01
45 103 0.81
46 23 0.18
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (45 bp):
GTCTTTCAACCATGGTCTTATTCGATAGAATCGTGATGCCATAAC
Found at i:27359177 original size:27 final size:27
Alignment explanation
Indices: 27359126--27359178 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
27359116 TACTTTACTT
* *
27359126 TTTATTAATTTATTAATTATTATTTAC
1 TTTATTAATTTATAAATTATCATTTAC
27359153 TTTATTAATTTA-AAATATATCATTTA
1 TTTATTAATTTATAAAT-TATCATTTA
27359179 AACTAACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTATTAATTTATAAATTATCATTTAC
Found at i:27380774 original size:109 final size:109
Alignment explanation
Indices: 27380572--27381040 Score: 625
Period size: 109 Copynumber: 4.3 Consensus size: 109
27380562 AAGGCTTTAA
* ****
27380572 TACAGCTTGTGTGAGCAGCATCGTGAGCCGGTGATTATTTAGCAGGTACTATGTGCCAGTGATAC
1 TACAGCTTGTGTGAGCAGCATCGTGAGCTGGTGATTATTTAGCAGGTACTATGTATGGGTGATAC
* *
27380637 AGACCGTAGCGATGGCTGAGACCCTGCATCTGTTGCGGATTCTC
66 AGACCGTAACGATGGCTGAGATCCTGCATCTGTTGCGGATTCTC
* * * * *
27380681 TACAGCTTGTGTGAGTAGCATCTTGAGTTGGTGATTATTTAGCAGGTACTACGTGCT-GGTGATA
1 TACAGCTTGTGTGAGCAGCATCGTGAGCTGGTGATTATTTAGCAGGTACTATGT-ATGGGTGATA
* * * * *
27380745 TAGACCGTAGCGATGGCTAAGATCTTGCATCTGTTGCAGATTCTC
65 CAGACCGTAACGATGGCTGAGATCCTGCATCTGTTGCGGATTCTC
* * * ***
27380790 TACATCTTGTGTGAGCAACAACGTGAGCCAATGATTATTTAGCAGGTACTATGTATGGGTGATAC
1 TACAGCTTGTGTGAGCAGCATCGTGAGCTGGTGATTATTTAGCAGGTACTATGTATGGGTGATAC
* *
27380855 AGACCGTAATGATGGCTGAGATCCTGCATTTGTTGCGGATTCTC
66 AGACCGTAACGATGGCTGAGATCCTGCATCTGTTGCGGATTCTC
*
27380899 TACAGCTTGTGTGAGCAGTATCGTGAGCTGGTGATTATTTAGCAGGTACTATGTATGGGTGATAC
1 TACAGCTTGTGTGAGCAGCATCGTGAGCTGGTGATTATTTAGCAGGTACTATGTATGGGTGATAC
* * * *
27380964 AGACCGTAATGATGGCTTGAGATCCTGCATTTCTTGCGGATTCTT
66 AGACCGTAACGATGGC-TGAGATCCTGCATCTGTTGCGGATTCTC
**
27381009 TGTAGCTTGTGTGAGCAGCATCGTGAGCTGGT
1 TACAGCTTGTGTGAGCAGCATCGTGAGCTGGT
27381041 CAAAGCTCTG
Statistics
Matches: 314, Mismatches: 43, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
108 1 0.00
109 258 0.82
110 55 0.18
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (109 bp):
TACAGCTTGTGTGAGCAGCATCGTGAGCTGGTGATTATTTAGCAGGTACTATGTATGGGTGATAC
AGACCGTAACGATGGCTGAGATCCTGCATCTGTTGCGGATTCTC
Found at i:27383745 original size:27 final size:27
Alignment explanation
Indices: 27383715--27383795 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
27383705 CTGGAGTAAC
*
27383715 GAGGGGAATGGTGATTTATCACATTTT
1 GAGGGGAATGGCGATTTATCACATTTT
27383742 GAGGGGAATGGCGATTTATCACATTTT
1 GAGGGGAATGGCGATTTATCACATTTT
27383769 GAGGGGAATGGCGATTTATCACATTTT
1 GAGGGGAATGGCGATTTATCACATTTT
27383796 TACTAGCAGC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.35
Consensus pattern (27 bp):
GAGGGGAATGGCGATTTATCACATTTT
Found at i:27384019 original size:10 final size:10
Alignment explanation
Indices: 27384004--27384035 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
27383994 ATTTATGATA
27384004 TGTGTTGTAT
1 TGTGTTGTAT
*
27384014 TGTGTTGTTT
1 TGTGTTGTAT
27384024 TGTGTTGTAT
1 TGTGTTGTAT
27384034 TG
1 TG
27384036 AATGGTATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.62
Consensus pattern (10 bp):
TGTGTTGTAT
Found at i:27386777 original size:45 final size:45
Alignment explanation
Indices: 27386726--27386830 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
27386716 TTCTAATGTA
* * *
27386726 GACAAAGCCACCAATACTCGCAAACTAGCTGCCATGTAGGTTGTG
1 GACAAAGCCACCAATACTCGCAAACAAACTACCATGTAGGTTGTG
* * *
27386771 GACAAAGCCACCAATATTTGCATACAAACTACCATGTAGGTTGTG
1 GACAAAGCCACCAATACTCGCAAACAAACTACCATGTAGGTTGTG
*
27386816 GACGAAGCCACCAAT
1 GACAAAGCCACCAAT
27386831 TCTTCCTCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (45 bp):
GACAAAGCCACCAATACTCGCAAACAAACTACCATGTAGGTTGTG
Found at i:27391025 original size:26 final size:25
Alignment explanation
Indices: 27390995--27391048 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
27390985 ATAATTAAGT
27390995 TTAAAATAAATTTAAA-ATATTTAATA
1 TTAAAATAAA-TTAAAGATATTTAA-A
* *
27391021 TTAAATTAAATTAAAGTTATTTAAA
1 TTAAAATAAATTAAAGATATTTAAA
27391046 TTA
1 TTA
27391049 TCTTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TTAAAATAAATTAAAGATATTTAAA
Found at i:27398213 original size:23 final size:24
Alignment explanation
Indices: 27398163--27398225 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
27398153 TCAATATATT
*
27398163 TTTATATTAAATAA--ATATAATTA
1 TTTATA-TAAATAATTATATAAATA
**
27398186 TTTATATATGTAATTATATAAATA
1 TTTATATAAATAATTATATAAATA
27398210 -TTATATAAATAATTAT
1 TTTATATAAATAATTAT
27398226 GTTATTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 5 0.15
23 20 0.61
24 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTATATAAATAATTATATAAATA
Found at i:27398214 original size:11 final size:12
Alignment explanation
Indices: 27398164--27398225 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
27398154 CAATATATTT
27398164 TTATATTAAATAA
1 TTATA-TAAATAA
* *
27398177 --ATATAATTAT
1 TTATATAAATAA
**
27398187 TTATATATGTAA
1 TTATATAAATAA
27398199 TTATATAAAT-A
1 TTATATAAATAA
27398210 TTATATAAATAA
1 TTATATAAATAA
27398222 TTAT
1 TTAT
27398226 GTTATTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.13
11 14 0.36
12 20 0.51
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TTATATAAATAA
Found at i:27398634 original size:23 final size:24
Alignment explanation
Indices: 27398584--27398646 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
27398574 TCAATATATT
*
27398584 TTTATATTAAATAA--ATATAATTA
1 TTTATA-TAAATAATTATATAAATA
**
27398607 TTTATATATGTAATTATATAAATA
1 TTTATATAAATAATTATATAAATA
27398631 -TTATATAAATAATTAT
1 TTTATATAAATAATTAT
27398647 GTTATTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 5 0.15
23 20 0.61
24 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTATATAAATAATTATATAAATA
Found at i:27398635 original size:11 final size:12
Alignment explanation
Indices: 27398585--27398646 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
27398575 CAATATATTT
27398585 TTATATTAAATAA
1 TTATA-TAAATAA
* *
27398598 --ATATAATTAT
1 TTATATAAATAA
**
27398608 TTATATATGTAA
1 TTATATAAATAA
27398620 TTATATAAAT-A
1 TTATATAAATAA
27398631 TTATATAAATAA
1 TTATATAAATAA
27398643 TTAT
1 TTAT
27398647 GTTATTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.13
11 14 0.36
12 20 0.51
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TTATATAAATAA
Found at i:27398930 original size:421 final size:422
Alignment explanation
Indices: 27398135--27398979 Score: 1683
Period size: 421 Copynumber: 2.0 Consensus size: 422
27398125 TTTAATTGTA
27398135 TATATTTAAGTAAATACATCAATATATTTTTATATTAAATAAATATAATTATTTATATATGTAAT
1 TATATTTAAGTAAATACATCAATATATTTTTATATTAAATAAATATAATTATTTATATATGTAAT
27398200 TATATAAATATTATATAAATAATTATGTTATTAATTTATAAAATTTGAATCAAGTAAAAACCATA
66 TATATAAATATTATATAAATAATTATGTTATTAATTTATAAAATTTGAATCAAGTAAAAACCATA
27398265 TATAGAGAATTACATAAAATCAAAATTAGTTGAACCCATAACCCCATAACCTTCTATATTGTATA
131 TATAGAGAATTACATAAAATCAAAATTAGTTGAACCCATAACCCCATAACCTTCTATATTGTATA
27398330 CAGAAACAGAAAATTTTAAATATTATTTTTTACTATCTAACAAATAAGGTGTCGTGGTGTAGTTG
196 CAGAAACAGAAAATTTTAAATATTATTTTTTACTATCTAACAAATAAGGTGTCGTGGTGTAGTTG
27398395 GTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGACGCCAAATCTTTTA
261 GTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGACGCCAAATCTTTTA
27398460 ATTTAAAGACGTTTTAGACGATCACGACGGGGGCCAGCTTTGATCAAACCCATATCCCACGTTTA
326 ATTTAAAGACGTTTTAGACGATCACGACGGGGGCCAGCTTTGATCAAACCCATATCCCACGTTTA
27398525 CTCCTTATTGGGCTCATGCCGACAGACCAAGC
391 CTCCTTATTGGGCTCATGCCGACAGACCAAGC
27398557 TATATTTAAG-AAATACATCAATATATTTTTATATTAAATAAATATAATTATTTATATATGTAAT
1 TATATTTAAGTAAATACATCAATATATTTTTATATTAAATAAATATAATTATTTATATATGTAAT
27398621 TATATAAATATTATATAAATAATTATGTTATTAATTTATAAAATTTGAATCAAGTAAAAACCATA
66 TATATAAATATTATATAAATAATTATGTTATTAATTTATAAAATTTGAATCAAGTAAAAACCATA
27398686 TATAGAGAATTACATAAAATCAAAATTAGTTGAACCCATAACCCCATAACCTTCTATATTGTATA
131 TATAGAGAATTACATAAAATCAAAATTAGTTGAACCCATAACCCCATAACCTTCTATATTGTATA
27398751 CAGAAACAGAAAATTTTAAATATTATTTTTTACTATCTAACAAATAAGGTGTCGTGGTGTAGTTG
196 CAGAAACAGAAAATTTTAAATATTATTTTTTACTATCTAACAAATAAGGTGTCGTGGTGTAGTTG
27398816 GTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGACGCCAAATCTTTTA
261 GTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGACGCCAAATCTTTTA
27398881 ATTTAAAGACGTTTTAGACGATCACGACGGGGGCCAGCTTTGATCAAACCCATATCCCACGTTTA
326 ATTTAAAGACGTTTTAGACGATCACGACGGGGGCCAGCTTTGATCAAACCCATATCCCACGTTTA
27398946 CTCCTTATTGGGCTCATGCCGACAGACCAAGC
391 CTCCTTATTGGGCTCATGCCGACAGACCAAGC
27398978 TA
1 TA
27398980 CTTTCTATTT
Statistics
Matches: 423, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
421 413 0.98
422 10 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (422 bp):
TATATTTAAGTAAATACATCAATATATTTTTATATTAAATAAATATAATTATTTATATATGTAAT
TATATAAATATTATATAAATAATTATGTTATTAATTTATAAAATTTGAATCAAGTAAAAACCATA
TATAGAGAATTACATAAAATCAAAATTAGTTGAACCCATAACCCCATAACCTTCTATATTGTATA
CAGAAACAGAAAATTTTAAATATTATTTTTTACTATCTAACAAATAAGGTGTCGTGGTGTAGTTG
GTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGACGCCAAATCTTTTA
ATTTAAAGACGTTTTAGACGATCACGACGGGGGCCAGCTTTGATCAAACCCATATCCCACGTTTA
CTCCTTATTGGGCTCATGCCGACAGACCAAGC
Found at i:27399191 original size:21 final size:24
Alignment explanation
Indices: 27399167--27399217 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 24
27399157 TTTTTATATA
27399167 TATTTTTATTTAT-GT-TGCATT-
1 TATTTTTATTTATCGTGTGCATTC
*
27399188 TA-TTTTATTTTTCGTGTGCATTC
1 TATTTTTATTTATCGTGTGCATTC
27399211 TATTTTT
1 TATTTTT
27399218 TTTTTACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.36
21 4 0.16
22 6 0.24
23 2 0.08
24 4 0.16
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.67
Consensus pattern (24 bp):
TATTTTTATTTATCGTGTGCATTC
Found at i:27399367 original size:17 final size:15
Alignment explanation
Indices: 27399347--27399385 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27399337 ATTTTTATTT
27399347 TTTAAAAATTTAATATA
1 TTTAAAAA-TT-ATATA
*
27399364 TTTATAAATTATATA
1 TTTAAAAATTATATA
27399379 TTTAAAA
1 TTTAAAA
27399386 GGCTTGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAAAAATTATATA
Found at i:27408424 original size:15 final size:15
Alignment explanation
Indices: 27408404--27408433 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27408394 GGGTCTATCC
27408404 CAACCTTTTTAAGGT
1 CAACCTTTTTAAGGT
27408419 CAACCTTTTTAAGGT
1 CAACCTTTTTAAGGT
27408434 TGGCATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
CAACCTTTTTAAGGT
Found at i:27408449 original size:50 final size:50
Alignment explanation
Indices: 27408369--27408463 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
27408359 ACGTTTACCC
* * *
27408369 CAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCC-AACCTTTTTAAGGT
1 CAACCTTTTTAAGGTTGCCATAGAAGGGTCTA-CCCTAAACTTTTTAAGGT
* *
27408419 CAACCTTTTTAAGGTTGGCATAGAATGGTCTACCCTAAACTTTTT
1 CAACCTTTTTAAGGTTGCCATAGAAGGGTCTACCCTAAACTTTTT
27408464 TTAGTCGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 3 0.08
50 36 0.92
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (50 bp):
CAACCTTTTTAAGGTTGCCATAGAAGGGTCTACCCTAAACTTTTTAAGGT
Found at i:27415351 original size:46 final size:46
Alignment explanation
Indices: 27415278--27416055 Score: 762
Period size: 46 Copynumber: 17.3 Consensus size: 46
27415268 NNNNNNNNNN
* *
27415278 AAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTTCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* * * *
27415324 AAATACAGGAAAACAAGATCTGTTATCTTCGATATCCTCTGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* *
27415370 AAATACAGGAAGACAAGATATGCTATCTTCGATCTCCTCCGTTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* * *
27415416 AAATATAGGAAGACAAGATCTGCTATCTTTGATCCCCTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* * * *
27415462 AAATATAGGAAGACAAGACCTGCTATCTTCGATCCCCTTCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* *
27415508 AAATATAGGAAGATAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* * *
27415554 AAATACAGGAAGATAAGATCTTCTATCTTCGATCTCCTCTGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* * * * * * ** * *
27415600 AAATACAGGAAGATAAGATATTCT-GCTGCCAAAT--ACAG--G--
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
** *** * * * ** *
27415639 AAGATA-A-G-ATCCGCTATCTTCGATC-TC-CTC-CGCTGCCAAAT-AC
1 AA-ATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CT-CC-GCTGCC
** *** *
27415682 AGGAGATA-A-G-ATTCTCTATCT-TTGATC-TC------CTCCGCTGCC
1 A--A-ATACAGGAAGACAAGATCTGCT-ATCTTCGATCTCCTCCGCTGCC
* *
27415721 AAATACAGGAAGACAAGATCTGTTATCTTCGATCTCCTCTGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
*
27415767 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCTTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* *
27415813 AAATACAGGAATACAAGATCTGCTATCTTCGATCCCCTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* *
27415859 AAATACAGAAAGACAAGATCTGCTATCTTCGATC-CCATCTGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCC-TCCGCTGCC
* * *
27415905 AAATACAGGAAGATAAGATCTACTATCTTCGATCTCCTCCGCTACC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
27415951 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
* *
27415997 AAATACAAGAAGATAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
27416043 AAATACAGGAAGA
1 AAATACAGGAAGA
27416056 ATCTGTTCTC
Statistics
Matches: 620, Mismatches: 84, Indels: 56
0.82 0.11 0.07
Matches are distributed among these distances:
36 3 0.00
37 9 0.01
38 4 0.01
39 17 0.03
40 9 0.01
41 1 0.00
43 3 0.00
45 28 0.05
46 544 0.88
47 2 0.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (46 bp):
AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC
Found at i:27415526 original size:138 final size:138
Alignment explanation
Indices: 27415278--27416055 Score: 1092
Period size: 138 Copynumber: 5.8 Consensus size: 138
27415268 NNNNNNNNNN
* * *
27415278 AAATACAGGAAGACAAGATCTACTATCTTCGATCTCCTTCGCTGCCAAATACAGGAAAACAAGAT
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
* * * *
27415343 CTGTTATCTTCGATATCCTCTGCTGCCAAATACAGGAAGACAAGATATGCTATCTTCGATCTCCT
66 CTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCCT
*
27415408 CCGTTGCC
131 CCGCTGCC
* * * * *
27415416 AAATATAGGAAGACAAGATCTGCTATCTTTGATCCCCTCCGCTGCCAAATATAGGAAGACAAGAC
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
* *
27415481 CTGCTATCTTCGATCCCCT-TCGCTGCCAAATATAGGAAGATAAGATCTGCTATCTTCGATCTCC
66 CTGCTATCTTCGATCTCCTCT-GCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCC
27415545 TCCGCTGCC
130 TCCGCTGCC
* * * *
27415554 AAATACAGGAAGATAAGATCTTCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGA-TA-A-
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
*
27415616 --G--A---T--A--T--TCTGCTGCCAAATACAGGAAGATAAGATCCGCTATCTTCGATCTCCT
66 CTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCCT
27415668 CCGCTGCC
131 CCGCTGCC
* *
27415676 AAATACAGG-AGATAAGATTCT-CTATCTTTGATCTCCTCCGCTGCCAAATACAGGAAGACAAGA
1 AAATACAGGAAGACAAGA-TCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGA
* * *
27415739 TCTGTTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCT
65 TCTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCC
27415804 TCCGCTGCC
130 TCCGCTGCC
* * *
27415813 AAATACAGGAATACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGAAAGACAAGAT
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
*
27415878 CTGCTATCTTCGATC-CCATCTGCTGCCAAATACAGGAAGATAAGATCTACTATCTTCGATCTCC
66 CTGCTATCTTCGATCTCC-TCTGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCC
*
27415942 TCCGCTACC
130 TCCGCTGCC
* *
27415951 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAAGAAGATAAGAT
1 AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
*
27416016 CTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGA
66 CTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGA
27416056 ATCTGTTCTC
Statistics
Matches: 569, Mismatches: 48, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
121 43 0.08
122 64 0.11
123 2 0.00
126 2 0.00
128 2 0.00
131 2 0.00
133 2 0.00
135 1 0.00
136 1 0.00
137 68 0.12
138 380 0.67
139 2 0.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (138 bp):
AAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGAT
CTGCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCTCCT
CCGCTGCC
Found at i:27415627 original size:30 final size:30
Alignment explanation
Indices: 27415591--27415648 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
27415581 TTCGATCTCC
27415591 TCTGCTGCCAAATACAGGAAGATAAGATAT
1 TCTGCTGCCAAATACAGGAAGATAAGATAT
27415621 TCTGCTGCCAAATACAGGAAGATAAGAT
1 TCTGCTGCCAAATACAGGAAGATAAGAT
27415649 CCGCTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (30 bp):
TCTGCTGCCAAATACAGGAAGATAAGATAT
Found at i:27415674 original size:76 final size:75
Alignment explanation
Indices: 27415548--27415693 Score: 256
Period size: 76 Copynumber: 1.9 Consensus size: 75
27415538 GATCTCCTCC
** *
27415548 GCTGCCAAATACAGGAAGATAAGATCTTCTATCTTCGATCTCCTCTGCTGCCAAATACAGGAAGA
1 GCTGCCAAATACAGGAAGATAAGATCCGCTATCTTCGATCTCCTCCGCTGCCAAATACAGG-AGA
27415613 TAAGATATTCT
65 TAAGATATTCT
27415624 GCTGCCAAATACAGGAAGATAAGATCCGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAGAT
1 GCTGCCAAATACAGGAAGATAAGATCCGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAGAT
27415689 AAGAT
66 AAGAT
27415694 TCTCTATCTT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 9 0.13
76 58 0.87
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (75 bp):
GCTGCCAAATACAGGAAGATAAGATCCGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGAGAT
AAGATATTCT
Found at i:27424030 original size:14 final size:14
Alignment explanation
Indices: 27424011--27424037 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27424001 GTTCAATTGT
27424011 ATACATTTAAATAA
1 ATACATTTAAATAA
27424025 ATACATTTAAATA
1 ATACATTTAAATA
27424038 TAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
ATACATTTAAATAA
Found at i:27426147 original size:13 final size:12
Alignment explanation
Indices: 27426106--27426171 Score: 59
Period size: 13 Copynumber: 5.6 Consensus size: 12
27426096 AATTTTGAAT
27426106 TATTTAGTGATAA
1 TATTTAGTGAT-A
* *
27426119 CATTTAG-AAT-
1 TATTTAGTGATA
27426129 TATTTAGTGATTA
1 TATTTAGTGA-TA
27426142 TATTTAG-GA-A
1 TATTTAGTGATA
27426152 TATTTAGTGATAA
1 TATTTAGTGAT-A
27426165 TATTTAG
1 TATTTAG
27426172 GAAAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 14 0.33
11 3 0.07
12 5 0.12
13 21 0.49
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (12 bp):
TATTTAGTGATA
Found at i:27426172 original size:23 final size:24
Alignment explanation
Indices: 27426102--27426174 Score: 114
Period size: 23 Copynumber: 3.1 Consensus size: 24
27426092 TTTAAATTTT
*
27426102 GAATTATTTAGTGATAACATTTA-
1 GAATTATTTAGTGATAATATTTAG
*
27426125 GAATTATTTAGTGATTATATTTAG
1 GAATTATTTAGTGATAATATTTAG
27426149 GAA-TATTTAGTGATAATATTTAG
1 GAATTATTTAGTGATAATATTTAG
27426172 GAA
1 GAA
27426175 AAATCTAGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 43 0.93
24 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (24 bp):
GAATTATTTAGTGATAATATTTAG
Found at i:27427098 original size:14 final size:14
Alignment explanation
Indices: 27427063--27427104 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
27427053 TTTGAATCTG
*
27427063 TTTTTATTTTATT-
1 TTTTTATTTTCTTA
27427076 TTTTGTATTTTCTTA
1 TTTT-TATTTTCTTA
*
27427091 TTTTTATTATCTTA
1 TTTTTATTTTCTTA
27427105 ATCAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTATTTTCTTA
Found at i:27428256 original size:30 final size:30
Alignment explanation
Indices: 27428213--27428281 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
27428203 TTCCATAGTA
* *
27428213 AAAAAGATTGATGAACTTACTAATGTGGTT
1 AAAAATATGGATGAACTTACTAATGTGGTT
27428243 AAAAATATGGATGAACTTACTAATGTGGTT
1 AAAAATATGGATGAACTTACTAATGTGGTT
27428273 AAAAATATG
1 AAAAATATG
27428282 CTTGCAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (30 bp):
AAAAATATGGATGAACTTACTAATGTGGTT
Found at i:27430050 original size:23 final size:23
Alignment explanation
Indices: 27430024--27430076 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
27430014 ATAAGTGTCA
27430024 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27430047 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
27430070 CACTGAT
1 CACTGAT
27430077 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:27430328 original size:18 final size:17
Alignment explanation
Indices: 27430302--27430340 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
27430292 ATTTTCCTTC
27430302 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
27430319 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
27430337 CACA
1 CACA
27430341 ATTTATANNN
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:27433143 original size:22 final size:20
Alignment explanation
Indices: 27433118--27433158 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
27433108 AAATATAAAA
27433118 ATACATAAAAAAATGTATATAG
1 ATACA-AAAAAAA-GTATATAG
*
27433140 ATACAAATAAAAGTATATA
1 ATACAAAAAAAAGTATATA
27433159 TTGGGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
ATACAAAAAAAAGTATATAG
Found at i:27433157 original size:20 final size:20
Alignment explanation
Indices: 27433102--27433158 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
27433092 CGTTTGAAAA
* *
27433102 AAATAAAAATATAAAAATAC
1 AAATAAAAGTATATAAATAC
* *
27433122 ATAAAAAAATGTATATAGATAC
1 A-AATAAAA-GTATATAAATAC
27433144 AAATAAAAGTATATA
1 AAATAAAAGTATATA
27433159 TTGGGTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.27
21 12 0.40
22 10 0.33
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (20 bp):
AAATAAAAGTATATAAATAC
Found at i:27434062 original size:13 final size:13
Alignment explanation
Indices: 27434044--27434109 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
27434034 AATTTTAAAT
27434044 TATTTAGTGATAA
1 TATTTAGTGATAA
*
27434057 TATTTA--GA-AT
1 TATTTAGTGATAA
*
27434067 TATTTAGTGATTA
1 TATTTAGTGATAA
27434080 TATTTAG-G--AA
1 TATTTAGTGATAA
27434090 TATTTAGTGATAA
1 TATTTAGTGATAA
27434103 TATTTAG
1 TATTTAG
27434110 GAAAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 15 0.35
11 3 0.07
12 3 0.07
13 22 0.51
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:27434110 original size:23 final size:24
Alignment explanation
Indices: 27434041--27434112 Score: 121
Period size: 23 Copynumber: 3.1 Consensus size: 24
27434031 TTAAATTTTA
27434041 AATTATTTAGTGATAATATTTA-G
1 AATTATTTAGTGATAATATTTAGG
*
27434064 AATTATTTAGTGATTATATTTAGG
1 AATTATTTAGTGATAATATTTAGG
27434088 AA-TATTTAGTGATAATATTTAGG
1 AATTATTTAGTGATAATATTTAGG
27434111 AA
1 AA
27434113 AAATCTAGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 43 0.93
24 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (24 bp):
AATTATTTAGTGATAATATTTAGG
Found at i:27435060 original size:5 final size:6
Alignment explanation
Indices: 27435044--27435068 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27435034 TAAACCCCCC
27435044 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
27435069 GCATTTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:27438306 original size:44 final size:46
Alignment explanation
Indices: 27438249--27438347 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 46
27438239 ATAGAAATAA
* * *
27438249 AGAAATGGAAAAT-ATTAAGAAATGATTATGGTTTTCTCCTAAATGG
1 AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCT-CAAAATGG
**
27438295 AGAAAT-G-AAATAATTTGGAAATAAATATGGTTTTCTCAAAAT-G
1 AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCTCAAAATGG
27438338 -GAAATGGAAA
1 AGAAATGGAAA
27438348 TGAAAATGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
42 5 0.11
43 2 0.04
44 11 0.24
45 21 0.47
46 6 0.13
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.30
Consensus pattern (46 bp):
AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCTCAAAATGG
Found at i:27440331 original size:28 final size:27
Alignment explanation
Indices: 27440300--27440354 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
27440290 AATAATTTTA
27440300 ACATTAAAACAAAATAATTT-TAAAAAAT
1 ACATT-AAA-AAAATAATTTATAAAAAAT
*
27440328 ACATTAAATAAATAATTTATAAAAAAT
1 ACATTAAAAAAATAATTTATAAAAAAT
27440355 TGTTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 11 0.44
28 5 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (27 bp):
ACATTAAAAAAATAATTTATAAAAAAT
Found at i:27443731 original size:44 final size:46
Alignment explanation
Indices: 27443674--27443772 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 46
27443664 ATAGAAATAA
* * *
27443674 AGAAATGGAAAAT-ATTAAGAAATGATTATGGTTTTCTCCTAAATGG
1 AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCT-CAAAATGG
**
27443720 AGAAAT-G-AAATAATTTGGAAATAAATATGGTTTTCTCAAAAT-G
1 AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCTCAAAATGG
27443763 -GAAATGGAAA
1 AGAAATGGAAA
27443773 TGAAAATGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
42 5 0.11
43 2 0.04
44 11 0.24
45 21 0.47
46 6 0.13
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.30
Consensus pattern (46 bp):
AGAAATGGAAAATAATTAAGAAATAAATATGGTTTTCTCAAAATGG
Found at i:27445756 original size:28 final size:27
Alignment explanation
Indices: 27445725--27445779 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
27445715 AATAATTTTA
27445725 ACATTAAAACAAAATAATTT-TAAAAAAT
1 ACATT-AAA-AAAATAATTTATAAAAAAT
*
27445753 ACATTAAATAAATAATTTATAAAAAAT
1 ACATTAAAAAAATAATTTATAAAAAAT
27445780 TGTTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 11 0.44
28 5 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (27 bp):
ACATTAAAAAAATAATTTATAAAAAAT
Found at i:27449148 original size:20 final size:20
Alignment explanation
Indices: 27449123--27449162 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27449113 CAACATTTTG
*
27449123 GATTAAATTTTGAATTTCAA
1 GATTAAATATTGAATTTCAA
27449143 GATTAAATATTGAATTTCAA
1 GATTAAATATTGAATTTCAA
27449163 AAGAGTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (20 bp):
GATTAAATATTGAATTTCAA
Found at i:27456367 original size:42 final size:42
Alignment explanation
Indices: 27456302--27456384 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
27456292 TATGCTTTAA
* ** *
27456302 AACCACACGGGCAAGGATGTGGACGTGTG-CATAGGCCGTGTG
1 AACCACACAGGCAAGGACATGGACGTATGTC-TAGGCCGTGTG
*
27456344 AACCACACAGGTAAGGACATGGACGTATGTCTAGGCCGTGT
1 AACCACACAGGCAAGGACATGGACGTATGTCTAGGCCGTGT
27456385 AGCATATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.34, T:0.18
Consensus pattern (42 bp):
AACCACACAGGCAAGGACATGGACGTATGTCTAGGCCGTGTG
Found at i:27466344 original size:81 final size:82
Alignment explanation
Indices: 27466208--27466371 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
27466198 TGTTTTAATA
27466208 TATGAGTTAATAACAAACTAAATTAATTTGTAATATTTAACCATTTTCATAACTTACTTTATACT
1 TATGAGTTAATAACAAACTAAATTAATTTGTAATATTTAACCATTTTCATAACTTACTTTATACT
27466273 AAAATTTTGTTATTACT
66 AAAATTTTGTTATTACT
27466290 TATGAGTTAAT-ACAAACTAAATTAATTTGTAATATTTAACCATTTTCATAACTTACTTTATACT
1 TATGAGTTAATAACAAACTAAATTAATTTGTAATATTTAACCATTTTCATAACTTACTTTATACT
27466354 AAAATTTTGTTATTACT
66 AAAATTTTGTTATTACT
27466371 T
1 T
27466372 TTATTTCTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.87
82 11 0.13
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (82 bp):
TATGAGTTAATAACAAACTAAATTAATTTGTAATATTTAACCATTTTCATAACTTACTTTATACT
AAAATTTTGTTATTACT
Found at i:27469908 original size:101 final size:101
Alignment explanation
Indices: 27469791--27469975 Score: 327
Period size: 101 Copynumber: 1.8 Consensus size: 101
27469781 AAAGTGATGG
*
27469791 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-AATGATAGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAATGAT-GGTCACATGTGTAGTA
27469855 CTATGTGCAGGCTACTATGCGTACCAGATAACTTTGA
65 CTATGTGCAGGCTACTATGCGTACCAGATAACTTTGA
*
27469892 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAATGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-AATGATGGTCACATGTGTAGTA
27469957 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
27469976 TGAATCGGTA
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
101 40 0.50
102 34 0.43
103 6 0.08
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAATGATGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCAGATAACTTTGA
Found at i:27469921 original size:51 final size:50
Alignment explanation
Indices: 27469788--27469973 Score: 248
Period size: 51 Copynumber: 3.7 Consensus size: 50
27469778 GTGAAAGTGA
* *
27469788 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGA-T
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-ATAATT
* * * *
27469838 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAACTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * *
27469889 TGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAATGA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAAT-T
27469940 TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
27469974 TGTGAATCGG
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
49 3 0.03
50 40 0.34
51 74 0.63
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:27474826 original size:11 final size:11
Alignment explanation
Indices: 27474810--27474834 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27474800 TTTCCATGCA
27474810 CAACTCAAACT
1 CAACTCAAACT
27474821 CAACTCAAACT
1 CAACTCAAACT
27474832 CAA
1 CAA
27474835 TGTACATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (11 bp):
CAACTCAAACT
Found at i:27478130 original size:15 final size:15
Alignment explanation
Indices: 27478107--27478155 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
27478097 GGAAGAGGTG
27478107 GAGAACTTGTTCGTT
1 GAGAACTTGTTCGTT
* *
27478122 GAGAGCTTG-T-GGT
1 GAGAACTTGTTCGTT
27478135 GAAGAACTTGTTCGTT
1 G-AGAACTTGTTCGTT
27478151 GAGAA
1 GAGAA
27478156 TTCGTGTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.11
14 8 0.30
15 13 0.48
16 3 0.11
ACGTcount: A:0.24, C:0.10, G:0.33, T:0.33
Consensus pattern (15 bp):
GAGAACTTGTTCGTT
Found at i:27479108 original size:18 final size:20
Alignment explanation
Indices: 27479072--27479108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27479062 ATAAAATGCA
*
27479072 TATATATATTAACTTTAATG
1 TATATATATTAACTATAATG
27479092 TATATATA-TAA-TATAAT
1 TATATATATTAACTATAAT
27479109 AATTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATATATTAACTATAATG
Found at i:27480360 original size:27 final size:27
Alignment explanation
Indices: 27480314--27480373 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
27480304 GTATGGTTGA
27480314 GAAATGGAAATGAGATGAGA-AAATATT
1 GAAATGGAAATGAGATGAGAGAAATA-T
27480341 GAAAT-GATAATGATGA-GAGATGAAATAT
1 GAAATGGA-AATGA-GATGAGA-GAAATAT
27480369 GAAAT
1 GAAAT
27480374 AGTATATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 8 0.28
29 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (27 bp):
GAAATGGAAATGAGATGAGAGAAATAT
Found at i:27490730 original size:43 final size:43
Alignment explanation
Indices: 27490637--27490722 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
27490627 CACATAAACA
* *
27490637 CCGCTAAAGAACATGAGCTTTAGCGGCACCTTTTTCACAAATG
1 CCGCTAAAGAACATGACCTTTAGCGACACCTTTTTCACAAATG
** *
27490680 CCGCTAAAGAACATGACCTTTAGCGATGCTTTTTTCACAAATG
1 CCGCTAAAGAACATGACCTTTAGCGACACCTTTTTCACAAATG
27490723 TTGCTAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
CCGCTAAAGAACATGACCTTTAGCGACACCTTTTTCACAAATG
Found at i:27496562 original size:43 final size:43
Alignment explanation
Indices: 27496514--27496669 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
27496504 CAAGTATAAT
27496514 TAAGTTATGTAAGTTATGATATGATAAATATTTATGTATTATG
1 TAAGTTATGTAAGTTATGATATGATAAATATTTATGTATTATG
*
27496557 TAAGTTATGTAAGTTTTGATATGATATATATTTATGTATTATGTTAGTTATG
1 TAAGTTATGTAAGTTATGATATGATA-A-A--TA--T-TTATG-TA-TTATG
* * * *
27496609 TAAGTGATGTGAGTTATGATATGATATATATTTATGAATTATG
1 TAAGTTATGTAAGTTATGATATGATAAATATTTATGTATTATG
*
27496652 TAAGTTATGTGAGTTATG
1 TAAGTTATGTAAGTTATG
27496670 TAAATTATAT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
43 47 0.48
44 2 0.02
45 6 0.06
46 1 0.01
47 2 0.02
48 2 0.02
49 1 0.01
50 6 0.06
51 2 0.02
52 28 0.29
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (43 bp):
TAAGTTATGTAAGTTATGATATGATAAATATTTATGTATTATG
Found at i:27496608 original size:52 final size:52
Alignment explanation
Indices: 27496545--27496681 Score: 190
Period size: 52 Copynumber: 2.7 Consensus size: 52
27496535 TGATAAATAT
* *
27496545 TTATG-TA-TTATGTAAGTTATGTAAGTTTTGATATGATATATATTTATGTA
1 TTATGTTAGTTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGAA
* *
27496595 TTATGTTAGTTATGTAAGTGATGTGAGTTATGATATGATATATATTTATGAA
1 TTATGTTAGTTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGAA
* * *
27496647 TTATGTAAGTTATGTGAGTTATGTAAATTAT-ATAT
1 TTATGTTAGTTATGTAAGTTATGTAAGTTATGATAT
27496682 TAATTTAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
50 5 0.07
51 6 0.08
52 65 0.86
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (52 bp):
TTATGTTAGTTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGAA
Found at i:27497055 original size:24 final size:24
Alignment explanation
Indices: 27497028--27497089 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 24
27497018 AATCAATTAA
*
27497028 TCAAATATAAAATCGATAATTTAT
1 TCAAATAAAAAATCGATAATTTAT
*
27497052 TCAATTAAATAAAAAATTGATAATTTAT
1 TC----AAATAAAAAATCGATAATTTAT
*
27497080 TCACATAAAA
1 TCAAATAAAA
27497090 TCAAATAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.29
28 22 0.71
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (24 bp):
TCAAATAAAAAATCGATAATTTAT
Found at i:27497115 original size:38 final size:38
Alignment explanation
Indices: 27497071--27497157 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
27497061 TAAAAAATTG
*
27497071 ATAATTTATTCACATAAAATCAAATAAACTAATCAAAC
1 ATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
* *
27497109 ATAATTTATTCACATTAAACCGAATAAACTAATCAAAC
1 ATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
27497147 AT-ATTTATTCA
1 ATAATTTATTCA
27497158 GTACAATCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 9 0.20
38 37 0.80
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (38 bp):
ATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
Found at i:27497185 original size:65 final size:66
Alignment explanation
Indices: 27497109--27497250 Score: 207
Period size: 65 Copynumber: 2.2 Consensus size: 66
27497099 CTAATCAAAC
* * *
27497109 ATAATTTATTCACATTAAACCGAATAAACTAATCAAACAT-ATTTATTCAGTACAATCGAAAA-T
1 ATAATTTATTCACATTAAACCGAATAAAATAATCAAACATAATTTATTCAAT-CAATCAAAAATT
27497172 CG
65 CG
* * *
27497174 ATAATTTATTCACATTAAATCGAATAAAATAATCAAACATAATTTATTCAATTAATTAAAAATTC
1 ATAATTTATTCACATTAAACCGAATAAAATAATCAAACATAATTTATTCAATCAATCAAAAATTC
27497239 G
66 G
27497240 ATAATTTATTC
1 ATAATTTATTC
27497251 TATTTAACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 45 0.65
66 24 0.35
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.35
Consensus pattern (66 bp):
ATAATTTATTCACATTAAACCGAATAAAATAATCAAACATAATTTATTCAATCAATCAAAAATTC
G
Found at i:27500051 original size:50 final size:50
Alignment explanation
Indices: 27499993--27500122 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
27499983 CCTAAGCGTA
**
27499993 TAAACCCTAAACCATAAACTTTACACCCTAAACTCTAAGTTCTTAACCTC
1 TAAACCCTAAACCATAAACTTTACACCCTAAACTCTAAGCCCTTAACCTC
* *
27500043 TAAACCCTAAATCATAAACTTTACACCCTAAACTCTAAGCCCTTAACCTT
1 TAAACCCTAAACCATAAACTTTACACCCTAAACTCTAAGCCCTTAACCTC
* * *
27500093 TAAACCTTAAACCCTAAAC-CTACACCCTAA
1 TAAACCCTAAACCATAAACTTTACACCCTAA
27500123 TCTGTAAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 10 0.14
50 62 0.86
ACGTcount: A:0.39, C:0.33, G:0.02, T:0.26
Consensus pattern (50 bp):
TAAACCCTAAACCATAAACTTTACACCCTAAACTCTAAGCCCTTAACCTC
Found at i:27500110 original size:7 final size:7
Alignment explanation
Indices: 27499963--27500181 Score: 62
Period size: 7 Copynumber: 31.0 Consensus size: 7
27499953 AAATCGGACA
*
27499963 CTAAACA
1 CTAAACC
27499970 CTAAACC
1 CTAAACC
*
27499977 ATAAACC
1 CTAAACC
* *
27499984 CTAAGCGT
1 CTAAAC-C
*
27499992 ATAAACC
1 CTAAACC
27499999 CTAAACC
1 CTAAACC
* *
27500006 ATAAACT
1 CTAAACC
* *
27500013 TTACACC
1 CTAAACC
*
27500020 CTAAACT
1 CTAAACC
***
27500027 CTAAGTT
1 CTAAACC
*
27500034 CTTAACC
1 CTAAACC
27500041 TCTAAACC
1 -CTAAACC
*
27500049 CTAAATC
1 CTAAACC
* *
27500056 ATAAACT
1 CTAAACC
* *
27500063 TTACACC
1 CTAAACC
*
27500070 CTAAACT
1 CTAAACC
*
27500077 CTAAGCC
1 CTAAACC
*
27500084 CTTAACC
1 CTAAACC
*
27500091 TTTAAACC
1 -CTAAACC
*
27500099 TTAAACC
1 CTAAACC
27500106 CTAAA-C
1 CTAAACC
*
27500112 CTACACC
1 CTAAACC
* *
27500119 CTAATCT
1 CTAAACC
* *
27500126 GTAAACA
1 CTAAACC
* *
27500133 CTAATCT
1 CTAAACC
* *
27500140 CTTAACA
1 CTAAACC
*
27500147 CTAAATC
1 CTAAACC
*
27500154 ATAAACC
1 CTAAACC
* *
27500161 TTAAATC
1 CTAAACC
*
27500168 TTAAACC
1 CTAAACC
27500175 CTAAACC
1 CTAAACC
27500182 ATAGACCTAA
Statistics
Matches: 145, Mismatches: 63, Indels: 8
0.67 0.29 0.04
Matches are distributed among these distances:
6 5 0.03
7 125 0.86
8 15 0.10
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26
Consensus pattern (7 bp):
CTAAACC
Found at i:27500121 original size:13 final size:14
Alignment explanation
Indices: 27500093--27500206 Score: 65
Period size: 14 Copynumber: 8.3 Consensus size: 14
27500083 CCTTAACCTT
27500093 TAAACCTTAAACCC
1 TAAACCTTAAACCC
*
27500107 TAAACC-TACACCC
1 TAAACCTTAAACCC
* *
27500120 T-AATCTGTAAACAC
1 TAAACCT-TAAACCC
* *
27500134 TAATCTCTT-AACAC
1 TAAAC-CTTAAACCC
* * *
27500148 TAAATCATAAACCT
1 TAAACCTTAAACCC
*
27500162 TAAATCTTAAACCC
1 TAAACCTTAAACCC
* *
27500176 TAAACCATAGA-CC
1 TAAACCTTAAACCC
* *
27500189 TAACCCTTAAACCT
1 TAAACCTTAAACCC
27500203 TAAA
1 TAAA
27500207 AATATATATT
Statistics
Matches: 73, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
12 3 0.04
13 19 0.26
14 47 0.64
15 2 0.03
16 2 0.03
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:27500205 original size:7 final size:7
Alignment explanation
Indices: 27500155--27500206 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
27500145 CACTAAATCA
27500155 TAAACCT
1 TAAACCT
*
27500162 TAAATCT
1 TAAACCT
*
27500169 TAAACCC
1 TAAACCT
*
27500176 TAAACCA
1 TAAACCT
*
27500183 TAGACC-
1 TAAACCT
*
27500189 TAACCCT
1 TAAACCT
27500196 TAAACCT
1 TAAACCT
27500203 TAAA
1 TAAA
27500207 AATATATATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 4 0.11
7 32 0.89
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:27500264 original size:7 final size:7
Alignment explanation
Indices: 27500254--27500313 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
27500244 ATCTTAAATA
27500254 CTAAACT
1 CTAAACT
*
27500261 CTAAACC
1 CTAAACT
*
27500268 CTAAACC
1 CTAAACT
*
27500275 CCAAACT
1 CTAAACT
27500282 CTAAAC-
1 CTAAACT
27500288 CATAAACT
1 C-TAAACT
27500296 CTAAACT
1 CTAAACT
*
27500303 CAAAACT
1 CTAAACT
27500310 CTAA
1 CTAA
27500314 TCTGAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 1 0.02
7 43 0.96
8 1 0.02
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACT
Found at i:27500392 original size:8 final size:8
Alignment explanation
Indices: 27500375--27500415 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
27500365 TTTAAATACT
27500375 AAACCCTA
1 AAACCCTA
*
27500383 AAACCTTA
1 AAACCCTA
27500391 AAACCCT-
1 AAACCCTA
*
27500398 AAACCAT-
1 AAACCCTA
27500405 AAACCCTA
1 AAACCCTA
27500413 AAA
1 AAA
27500416 TAAAGCTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.15
Consensus pattern (8 bp):
AAACCCTA
Found at i:27500401 original size:15 final size:14
Alignment explanation
Indices: 27500374--27500414 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
27500364 CTTTAAATAC
*
27500374 TAAACCCTAAAACCT
1 TAAACCCT-AAACCA
27500389 TAAAACCCTAAACCA
1 T-AAACCCTAAACCA
27500404 TAAACCCTAAA
1 TAAACCCTAAA
27500415 ATAAAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 10 0.42
15 7 0.29
16 7 0.29
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:27500663 original size:40 final size:41
Alignment explanation
Indices: 27500619--27500701 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 41
27500609 CGCTTTCTGT
**
27500619 AAAGCACCGCT-ATTGCTTGATCTTTAGCCGCGTTT-TTAAA
1 AAAGCACCGCTAATT-CTCAATCTTTAGCCGCGTTTGTTAAA
* * *
27500659 AAAGCGCCGCTAATTCTCAATCTTTTGCGGCGTTTGTTAAA
1 AAAGCACCGCTAATTCTCAATCTTTAGCCGCGTTTGTTAAA
27500700 AA
1 AA
27500702 GGGCCACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 26 0.72
41 10 0.28
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (41 bp):
AAAGCACCGCTAATTCTCAATCTTTAGCCGCGTTTGTTAAA
Found at i:27500807 original size:40 final size:39
Alignment explanation
Indices: 27500765--27500904 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 39
27500755 ACTTTTTTGT
*
27500765 GGCATTTTCCAAAAAGCGCCGCTATTGCTTGATCTATAGT
1 GGCATTTTCCAAAAAGCGCCGCTATT-CTTGATCTATAGC
* * * *
27500805 GGCA-TTTCTCAAAAATCACCACTATTTCTTTATCTATAGC
1 GGCATTTTC-CAAAAAGCGCCGCTA-TTCTTGATCTATAGC
* * * *
27500845 GGCATTTTTCAAAAAGCGTCGCAAATTCTTGATCTATTGC
1 GGCATTTTCCAAAAAGCGCCGC-TATTCTTGATCTATAGC
*
27500885 GGCATTTGT-TAAAAAGCGCC
1 GGCATTT-TCCAAAAAGCGCC
27500905 ATTAATGCCA
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
39 4 0.05
40 69 0.86
41 7 0.09
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (39 bp):
GGCATTTTCCAAAAAGCGCCGCTATTCTTGATCTATAGC
Found at i:27500887 original size:198 final size:196
Alignment explanation
Indices: 27500453--27501072 Score: 629
Period size: 190 Copynumber: 3.2 Consensus size: 196
27500443 CTTTTTTTGT
* * * * **
27500453 GGCATTTTACAAAAAGCACCACTAATTCTCGTTCTATTGCGATGTTTGTTAAAAAGCGCCACTAA
1 GGCATTTTTCAAAAAGCGCCGCTAATTCTCGATCTATTGCGGCGTTTGTTAAAAAGCGCCACTAA
* *
27500518 TGCCACTAAAGCTCAAAAAG--AA-AATGTCGTTTTGCTCAACTTTTTTGCGGCATTTTCCAACA
66 TGCCACTAAAGCTCAAAAAGAAAACAATGTCGTTTTGCTCAACTTTTTTGTGGCATTTTCCAAAA
* * ** * *
27500580 ACCGCCCGCTAATGCTTGATCTATAGCGGCGCTTTCTGTAAAGCACCGCTATTGCTTGATCTTTA
131 AGCG-CCGCTAATGCTTGATCTATAGCGGCGATTTCTAAAAAGCACCACTATTGCTTGATCTATA
27500645 GC
195 GC
* * * * * *
27500647 CGCGTTTTTAAAAAAGCGCCGCTAATTCTCAATCTTTTGCGGCGTTTGTTAAAAAGGGCCACTAA
1 GGCATTTTTCAAAAAGCGCCGCTAATTCTCGATCTATTGCGGCGTTTGTTAAAAAGCGCCACTAA
* * * *
27500712 TGACCCCCTAAAACTCAAAAAGAAAACAATGTCATGTTGCTCAACTTTTTTGTGGCATTTTCCAA
66 TG--CCACTAAAGCTCAAAAAGAAAACAATGTCGTTTTGCTCAACTTTTTTGTGGCATTTTCCAA
* * * * *
27500777 AAAGCGCCGCTATTGCTTGATCTATAGTGGC-ATTTCTCAAAAATCACCACTATTTCTTTATCTA
129 AAAGCGCCGCTAATGCTTGATCTATAGCGGCGATTTCT-AAAAAGCACCACTATTGCTTGATCTA
27500841 TAGC
193 TAGC
* * * * *
27500845 GGCATTTTTCAAAAAGCGTCGCAAATTCTTGATCTATTGCGGCATTTGTTAAAAAGCGCCATTAA
1 GGCATTTTTCAAAAAGCGCCGCTAATTCTCGATCTATTGCGGCGTTTGTTAAAAAGCGCCACTAA
* * * *
27500910 TGCCACTAAAGCTC------AAAACAATGACGTTTTGCTAAACTTTATTGTGGCGTTTTCCAAAA
66 TGCCACTAAAGCTCAAAAAGAAAACAATGTCGTTTTGCTCAACTTTTTTGTGGCATTTTCCAAAA
* * * * * *
27500969 AGCACCGTTAATGCTTGATATATAGCGGCG-TTT-TACACTAAA-CGCCGCTATTGCTTGATCTT
131 AGCGCCGCTAATGCTTGATCTATAGCGGCGATTTCTA-A--AAAGCACCACTATTGCTTGATCTA
*
27501031 TAGT
193 TAGC
* * * *
27501035 GGCGTTTGTT-AAAAAGCGCCACTAATGCTCGATTTATT
1 GGCATTT-TTCAAAAAGCGCCGCTAATTCTCGATCTATT
27501073 ACGACATTTT
Statistics
Matches: 349, Mismatches: 66, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
188 1 0.00
189 2 0.01
190 112 0.32
191 5 0.01
194 55 0.16
196 26 0.07
197 5 0.01
198 104 0.30
199 39 0.11
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (196 bp):
GGCATTTTTCAAAAAGCGCCGCTAATTCTCGATCTATTGCGGCGTTTGTTAAAAAGCGCCACTAA
TGCCACTAAAGCTCAAAAAGAAAACAATGTCGTTTTGCTCAACTTTTTTGTGGCATTTTCCAAAA
AGCGCCGCTAATGCTTGATCTATAGCGGCGATTTCTAAAAAGCACCACTATTGCTTGATCTATAG
C
Found at i:27501051 original size:190 final size:189
Alignment explanation
Indices: 27500497--27501054 Score: 600
Period size: 198 Copynumber: 2.9 Consensus size: 189
27500487 TATTGCGATG
*
27500497 TTTGTTAAAAAGCGCCACTAATGCCACTAAAGCTCAAAAAGAAAATGTCGTTTTGCTCAACTTTT
1 TTTGTTAAAAAGCGCCACTAATGCCACTAAAGCTC-AAAA-ACAATGTCGTTTTGCTCAACTTTT
* * * *
27500562 TTGCGGCATTTTCCAACAACCGCCCGCTAATGCTTGATCTATAGCGGCGCTTTCTGTAAAGCACC
64 TTGTGGCATTTTCCAA-AA-AGCCCGCTAATGCTTGATCTATAGCGGCGTTTTC-ATAAAGCACC
* * * *
27500627 GCTATTGCTTGATCTTTAGCCGCGTTTTTAAAAAAGCGCCGCTAATTCTCAATCTTTTGCGGCG
126 GCTATTGCTTGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCAAATTCTCAATCTATTGCGGCA
* * * * *
27500691 TTTGTTAAAAAGGGCCACTAATGACCCCCTAAAACTCAAAAAGAAAACAATGTCATGTTGCTCAA
1 TTTGTTAAAAAGCGCCACTAATG--CCACTAAAGCTC----A-AAAACAATGTCGTTTTGCTCAA
* * * * *
27500756 CTTTTTTGTGGCATTTTCCAAAAAGCGCCGCTATTGCTTGATCTATAGTGGCATTTCTCAAAAAT
59 CTTTTTTGTGGCATTTTCCAAAAAGC-CCGCTAATGCTTGATCTATAGCGGCGTTT-TCATAAAG
* * * * * * * **
27500821 CACCACTATTTCTTTATCTATAGCGGCATTTTTCAAAAAGCGTCGCAAATTCTTGATCTATTGCG
122 CACCGCTATTGCTTGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCAAATTCTCAATCTATTGCG
27500886 GCA
187 GCA
* * * *
27500889 TTTGTTAAAAAGCGCCATTAATGCCACTAAAGCTC-AAAACAATGACGTTTTGCTAAACTTTATT
1 TTTGTTAAAAAGCGCCACTAATGCCACTAAAGCTCAAAAACAATGTCGTTTTGCTCAACTTTTTT
* * * *
27500953 GTGGCGTTTTCCAAAAAGCACCGTTAATGCTTGATATATAGCGGCGTTTTACACTAAA-CGCCGC
66 GTGGCATTTTCCAAAAAGC-CCGCTAATGCTTGATCTATAGCGGCGTTTT-CA-TAAAGCACCGC
*
27501017 TATTGCTTGATCTTTAGTGGCGTTTGTT-AAAAAGCGCC
128 TATTGCTTGATCTTTAGCGGCGTTT-TTAAAAAAGCGCC
27501055 ACTAATGCTC
Statistics
Matches: 300, Mismatches: 53, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
189 1 0.00
190 101 0.34
191 5 0.02
194 22 0.07
196 20 0.07
197 2 0.01
198 106 0.35
199 40 0.13
200 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (189 bp):
TTTGTTAAAAAGCGCCACTAATGCCACTAAAGCTCAAAAACAATGTCGTTTTGCTCAACTTTTTT
GTGGCATTTTCCAAAAAGCCCGCTAATGCTTGATCTATAGCGGCGTTTTCATAAAGCACCGCTAT
TGCTTGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCAAATTCTCAATCTATTGCGGCA
Found at i:27508958 original size:24 final size:24
Alignment explanation
Indices: 27508931--27508979 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27508921 TTTTTGTAGG
27508931 ACATAGATTAATAAATATCTTTAT
1 ACATAGATTAATAAATATCTTTAT
27508955 ACATAGATTAATAAATATCTTTAT
1 ACATAGATTAATAAATATCTTTAT
27508979 A
1 A
27508980 ATGCATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (24 bp):
ACATAGATTAATAAATATCTTTAT
Found at i:27509614 original size:27 final size:27
Alignment explanation
Indices: 27509576--27509631 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
27509566 TTAACACTTA
27509576 TTGCAACATTTATAAACAAAACTATGG
1 TTGCAACATTTATAAACAAAACTATGG
27509603 TTGCAACATTTATAAACAAAACTATGG
1 TTGCAACATTTATAAACAAAACTATGG
27509630 TT
1 TT
27509632 AAACCAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (27 bp):
TTGCAACATTTATAAACAAAACTATGG
Done.