Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 51 of 444
Found at i:12255004 original size:16 final size:17
Alignment explanation
Indices: 12254973--12255005 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12254963 TTCATAAGTA
12254973 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
*
12254990 TATATGAAT-ATTTCAT
1 TATATCAATCATTTCAT
12255006 GCTCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:12255351 original size:46 final size:46
Alignment explanation
Indices: 12255286--12255545 Score: 283
Period size: 46 Copynumber: 5.7 Consensus size: 46
12255276 TTATCTTTGA
* * * *
12255286 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* **
12255332 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGT
* ** * * *
12255378 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* * * *
12255423 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
* * *
12255469 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACGT-ATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTTCTGT
* *
12255515 CCTGTTGCCATGCTATCTTTCAACCATGGTC
1 CATGTTGCCATGGTATCTTTCAACCATGGTC
12255546 CTACAATTTT
Statistics
Matches: 184, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 38 0.21
46 146 0.79
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGT
Found at i:12255454 original size:91 final size:92
Alignment explanation
Indices: 12255291--12255554 Score: 275
Period size: 91 Copynumber: 2.9 Consensus size: 92
12255281 TTTGACATGA
* * * * *
12255291 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTATCTTTCAAC
*** *
12255356 CATGGTCTTGTTCATTTCATGTTAC-AT
66 CATGGTCTTACACATTTCAT-ATACTAT
* * *
12255383 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGTCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTATCTTTCAAC
* * *
12255447 CATGGTCTTACACATTTTATATCCTGT
66 CATGGTCTTACACATTTCATATACTAT
**** ** *
12255474 TGCCATGGTATCTTTCAACCATGGTCTTACGT-ATTTTATATCCTGTTGCCATGCTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCCCGTCAGGTTGCCATGGTATCTTTCAA
*
12255538 CCATGGTCCTACA-ATTT
65 CCATGGTCTTACACATTT
12255555 TCATTTCAGA
Statistics
Matches: 145, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
90 2 0.01
91 78 0.54
92 65 0.45
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATACTAT
Found at i:12259446 original size:20 final size:20
Alignment explanation
Indices: 12259421--12259459 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12259411 TGATGAATAA
* *
12259421 AAGAAACAGGGAAAAGTTTG
1 AAGAAAAAGGAAAAAGTTTG
12259441 AAGAAAAAGGAAAAAGTTT
1 AAGAAAAAGGAAAAAGTTT
12259460 CGGAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (20 bp):
AAGAAAAAGGAAAAAGTTTG
Found at i:12260649 original size:46 final size:45
Alignment explanation
Indices: 12260432--12260649 Score: 178
Period size: 46 Copynumber: 4.7 Consensus size: 45
12260422 GGTTATTATA
* *
12260432 AGCTAGTATAAGACATGTCTGGGACATGCATCGGCCACATTATGA-G-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA--A-GACGT
* * * * **
12260478 AGCCAGTATAAGACCATGTTTGGGACATGTCATCGGCATTGAGACG-
1 AGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCAAGACGT
*
12260524 AGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
1 A--GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGT
* *
12260571 AAGCTAGTATAAGACATGTCTGGGACATGCATCGG-CTACAAGATGT
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CAAGACGT
*
12260617 -G-TCAGTGTAAGACAATGTCTAGGACATGGCATC
1 AGCT-AGTGTAAGAC-ATGTCTGGGACAT-GCATC
12260650 AGAACAGATA
Statistics
Matches: 145, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 10 0.07
45 16 0.11
46 72 0.50
47 28 0.19
48 18 0.12
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGT
Found at i:12263194 original size:16 final size:15
Alignment explanation
Indices: 12263173--12263230 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
12263163 TTGGTAAATT
*
12263173 AAAAAATTAAGTGTTG
1 AAAAAA-TAAGTATTG
*
12263189 AAAAAATAAATATTG
1 AAAAAATAAGTATTG
12263204 AAAATAATAAGTATTG
1 AAAA-AATAAGTATTG
* *
12263220 ATAAATTAAGT
1 AAAAAATAAGT
12263231 GTAGAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 17 0.47
16 19 0.53
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (15 bp):
AAAAAATAAGTATTG
Found at i:12265379 original size:26 final size:26
Alignment explanation
Indices: 12265332--12265384 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12265322 TTTCTTTAGT
* * *
12265332 TTATATATATAATATAATATAATATA
1 TTATATATATAATAAAACATAAAATA
12265358 TTATAT-TATAATTAAAACATAAAATA
1 TTATATATATAA-TAAAACATAAAATA
12265384 T
1 T
12265385 CTTTGTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTATATATATAATAAAACATAAAATA
Found at i:12265515 original size:39 final size:39
Alignment explanation
Indices: 12265471--12265564 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
12265461 ATACTTTTAG
**
12265471 TATAATTGTCCTTTTAGTCCTTTTTATTTTCTTTTAATC
1 TATAATTCACCTTTTAGTCCTTTTTATTTTCTTTTAATC
12265510 TATAATTCACCTTTTAGTCCTTTTTATTTTCTTTTAATC
1 TATAATTCACCTTTTAGTCCTTTTTATTTTCTTTTAATC
*
12265549 TATAATTCAACTTTTA
1 TATAATTCACCTTTTA
12265565 CCCTTTATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (39 bp):
TATAATTCACCTTTTAGTCCTTTTTATTTTCTTTTAATC
Found at i:12272082 original size:17 final size:16
Alignment explanation
Indices: 12272020--12272082 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 16
12272010 CTTAAATTTC
* * *
12272020 TTCTTTTCTTTTTTTT
1 TTCTTTTCCTTTCTGT
12272036 TTCTTTT-CTTTCTGT
1 TTCTTTTCCTTTCTGT
* *
12272051 TTCGTTCCCTATTCTGT
1 TTCTTTTCCT-TTCTGT
12272068 TTCTATTTCCTTTCT
1 TTCT-TTTCCTTTCT
12272083 TTTATTTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 10 0.27
16 9 0.24
17 13 0.35
18 5 0.14
ACGTcount: A:0.03, C:0.22, G:0.05, T:0.70
Consensus pattern (16 bp):
TTCTTTTCCTTTCTGT
Found at i:12272140 original size:29 final size:28
Alignment explanation
Indices: 12272101--12272184 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
12272091 TTTAGTTTAT
* *
12272101 ATATATAATATAATAATTAATACAATATA
1 ATATATTATATAATAATTAATAC-ATAAA
* *
12272130 ATATATTATATTATAATTAAAACATAAA
1 ATATATTATATAATAATTAATACATAAA
12272158 ATATCTTTATTATATAATAATATAATA
1 ATA----TATTATATAATAAT-TAATA
12272185 ATATATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.16
29 20 0.45
32 13 0.30
33 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATATTATATAATAATTAATACATAAA
Found at i:12272175 original size:44 final size:42
Alignment explanation
Indices: 12272125--12272206 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
12272115 AATTAATACA
* *
12272125 ATATAAT-ATATTATATTATAATTAAAACATAAAATATCTTTATT
1 ATATAATAATATAATAATAT-ATT-AAACATAAAA-ATCTTTATT
12272169 ATATAATAATATAATAATATATTAAACATAAAAATCTT
1 ATATAATAATATAATAATATATTAAACATAAAAATCTT
12272207 AGATTTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 5 0.14
43 10 0.29
44 10 0.29
45 10 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (42 bp):
ATATAATAATATAATAATATATTAAACATAAAAATCTTTATT
Found at i:12274580 original size:12 final size:12
Alignment explanation
Indices: 12274561--12274592 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
12274551 TAACAATAAT
12274561 TTTAAAAAAATTC
1 TTTAAAAAAA-TC
12274574 TTTAAAAAAATC
1 TTTAAAAAAATC
12274586 TTTAAAA
1 TTTAAAA
12274593 GTTCAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTAAAAAAATC
Found at i:12279473 original size:8 final size:8
Alignment explanation
Indices: 12279460--12279485 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12279450 TTTTCAAAAT
12279460 ATATATTC
1 ATATATTC
12279468 ATATATTC
1 ATATATTC
12279476 ATATATTC
1 ATATATTC
12279484 AT
1 AT
12279486 TGGCCTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATTC
Found at i:12281267 original size:19 final size:19
Alignment explanation
Indices: 12281229--12281269 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12281219 TAAATTAAGA
*
12281229 AAATATTAAAAATAATATT
1 AAATATTAAAAATAACATT
* *
12281248 AAATATTAAATATTACATT
1 AAATATTAAAAATAACATT
12281267 AAA
1 AAA
12281270 AAGAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATTAAAAATAACATT
Found at i:12298904 original size:20 final size:20
Alignment explanation
Indices: 12298876--12298924 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
12298866 CATTTATCTT
* *
12298876 ATTTTATTTTATTTCAATCA
1 ATTTGATTTTATTTCAACCA
*
12298896 ATTTGATTTTATTTTAACCA
1 ATTTGATTTTATTTCAACCA
*
12298916 AATTGATTT
1 ATTTGATTT
12298925 ATTAGCTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTGATTTTATTTCAACCA
Found at i:12299307 original size:14 final size:14
Alignment explanation
Indices: 12299270--12299308 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12299260 TTAGTAAAAT
**
12299270 TTTATATATAAATA
1 TTTATATATTTATA
*
12299284 TTTATTTATTTATA
1 TTTATATATTTATA
12299298 TTTATATATTT
1 TTTATATATTT
12299309 TGTTCGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:12300962 original size:3 final size:3
Alignment explanation
Indices: 12300956--12301011 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
12300946 TCAATATGTC
12300956 ATA ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12301002 ATA ATA ATA A
1 ATA ATA ATA A
12301012 AGAACAAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12302252 original size:15 final size:15
Alignment explanation
Indices: 12302232--12302261 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12302222 TTTAATCCTT
*
12302232 TATAAATTATAAAAA
1 TATAAACTATAAAAA
12302247 TATAAACTATAAAAA
1 TATAAACTATAAAAA
12302262 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:12302706 original size:14 final size:14
Alignment explanation
Indices: 12302687--12302717 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12302677 TTAATTAATT
12302687 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
12302701 TTTAATTAATTAAA
1 TTTAATTAAATAAA
12302715 TTT
1 TTT
12302718 TATAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:12304146 original size:31 final size:30
Alignment explanation
Indices: 12304111--12304214 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
12304101 AAAAATTGGG
*
12304111 AAATTTTGATTTCTCCATTGAAATTTTTAGA
1 AAATTTTAATTTCTCC-TTGAAATTTTTAGA
* * * * *
12304142 AAATTTTAATTAAGC-CCGTCAAAATTTTCGA
1 AAATTTTAATT--TCTCCTTGAAATTTTTAGA
* *
12304173 AAATTTTCATTTCTCTCTTGAAGTTTTTAGA
1 AAATTTTAATTTCTC-CTTGAAATTTTTAGA
*
12304204 AAAATTTAATT
1 AAATTTTAATT
12304215 AGGCCCCCTC
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
29 1 0.02
30 1 0.02
31 49 0.91
32 2 0.04
33 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (30 bp):
AAATTTTAATTTCTCCTTGAAATTTTTAGA
Found at i:12304229 original size:62 final size:62
Alignment explanation
Indices: 12304111--12304236 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 62
12304101 AAAAATTGGG
* * *
12304111 AAATTTTGATTTCTCCATTGAAATTTTTAGAAAATTTTAATTAAGCCCGTCAAAATTTTCGA
1 AAATTTTCATTTCTCCATTGAAATTTTTAGAAAAATTTAATTAAGCCCCTCAAAATTTTCGA
* * *
12304173 AAATTTTCATTTCTCTC-TTGAAGTTTTTAGAAAAATTTAATTAGGCCCCCTC-AAATTTTTGA
1 AAATTTTCATTTCTC-CATTGAAATTTTTAGAAAAATTTAATTAAG-CCCCTCAAAATTTTCGA
12304235 AA
1 AA
12304237 CTTTCTTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 50 0.89
63 6 0.11
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (62 bp):
AAATTTTCATTTCTCCATTGAAATTTTTAGAAAAATTTAATTAAGCCCCTCAAAATTTTCGA
Found at i:12304498 original size:31 final size:31
Alignment explanation
Indices: 12304463--12304546 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
12304453 AAAATTTTAG
* *
12304463 AATTCGAAAAGTATAGGGACTAAAATTGA-CC
1 AATTC-AAAAGTATAAGGACTAAAATTGATCA
* *
12304494 AATTCAAAAAGTACAATGACTAAAATTGATCA
1 AATTC-AAAAGTATAAGGACTAAAATTGATCA
*
12304526 AATT--AAAGTATATGGACTAAA
1 AATTCAAAAGTATAAGGACTAAA
12304547 TCATAACTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 14 0.32
31 25 0.57
32 5 0.11
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (31 bp):
AATTCAAAAGTATAAGGACTAAAATTGATCA
Found at i:12306721 original size:154 final size:156
Alignment explanation
Indices: 12306438--12306791 Score: 525
Period size: 154 Copynumber: 2.3 Consensus size: 156
12306428 TTAGAGTTTT
* * * *
12306438 TAATTAAATTAAATTTTCCCTTAAAAAATACTAAAATCCTAAACTATTAAAACCCTAATCCCAAA
1 TAATTAAATTAAATTTTCTCTT-AAAAATACTAAAACCCTAAACCACTAAAACCCTAATCCCAAA
*
12306503 ATAATAAAAAACCCTAACCTTAAAAAACCCTAAACCCTAATCTAATTGATTTTTTAATTTCATAG
65 ATAATAAAAAACCATAACCTTAAAAAACCCTAAACCCTAATCTAATTGATTTTTTAATTTCATAG
*
12306568 TTAATTTAATTAATTAACTCTCAACTC
130 TTAATTTAATTAATTAACCCTCAACTC
* * *
12306595 TAATTAAATTAACTTTTCTCTT-AAAATAATAAAACCCTAAACCACT-AAACCCTAATCCTAAAA
1 TAATTAAATTAAATTTTCTCTTAAAAATACTAAAACCCTAAACCACTAAAACCCTAATCCCAAAA
* *
12306658 TAATCAAAAACCATAACCTTAAAAAACCCTAAACCCTAATTTAATT-ATTTTTTTAATTTCATAG
66 TAATAAAAAACCATAACCTTAAAAAACCCTAAACCCTAATCTAATTGA-TTTTTTAATTTCATAG
*
12306722 TTAATTTAATTAATTAACCCTTAACTC
130 TTAATTTAATTAATTAACCCTCAACTC
* **
12306749 TAATTAAACTATTTTTTCTCTTAAAAAATACTAAAACCCTAAA
1 TAATTAAATTAAATTTTCTCTT-AAAAATACTAAAACCCTAAA
12306792 TCTTAAAAAT
Statistics
Matches: 178, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
153 1 0.01
154 119 0.67
155 20 0.11
156 18 0.10
157 20 0.11
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (156 bp):
TAATTAAATTAAATTTTCTCTTAAAAATACTAAAACCCTAAACCACTAAAACCCTAATCCCAAAA
TAATAAAAAACCATAACCTTAAAAAACCCTAAACCCTAATCTAATTGATTTTTTAATTTCATAGT
TAATTTAATTAATTAACCCTCAACTC
Found at i:12314572 original size:38 final size:38
Alignment explanation
Indices: 12314521--12314596 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
12314511 TGTATTTTTC
*
12314521 ATGTTATGATCCTTATAAAATATGGAACAAGTGAGGAT
1 ATGTTATGATCCTTACAAAATATGGAACAAGTGAGGAT
12314559 ATGTTATGATCCTTACAAAATATGGAACAAGTGAGGAT
1 ATGTTATGATCCTTACAAAATATGGAACAAGTGAGGAT
12314597 GGTGGTGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (38 bp):
ATGTTATGATCCTTACAAAATATGGAACAAGTGAGGAT
Found at i:12323023 original size:24 final size:26
Alignment explanation
Indices: 12322996--12323046 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
12322986 TTTTTAATAG
12322996 TTTATAAGT-T-ATAAATAATTTTA-
1 TTTATAAGTATAATAAATAATTTTAC
*
12323019 TTT-TAAGTATAATAATTAATTTTAC
1 TTTATAAGTATAATAAATAATTTTAC
12323044 TTT
1 TTT
12323047 TACTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 12 0.50
25 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTATAAGTATAATAAATAATTTTAC
Found at i:12331483 original size:15 final size:16
Alignment explanation
Indices: 12331448--12331486 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
12331438 AACCTGCAAA
*
12331448 AAAATCAATGTTATAAG
1 AAAATC-ATGTCATAAG
12331465 AAAATCATGTCAT-AG
1 AAAATCATGTCATAAG
12331480 AAAATCA
1 AAAATCA
12331487 GTGTTATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 6 0.29
17 6 0.29
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAATCATGTCATAAG
Found at i:12332158 original size:23 final size:23
Alignment explanation
Indices: 12332128--12332172 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
12332118 GAGCTTAAAC
*
12332128 TTTTAATTTT-TTTAATAATTTA
1 TTTTAATTTTATTCAATAATTTA
12332150 TTTTGAATTTTATTCAATAATTT
1 TTTT-AATTTTATTCAATAATTT
12332173 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTAATTTTATTCAATAATTTA
Found at i:12332198 original size:19 final size:18
Alignment explanation
Indices: 12332165--12332224 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
12332155 AATTTTATTC
* *
12332165 AATAATTTTAAAAATTTT
1 AATATTTTTTAAAATTTT
12332183 AATATTTTTTACAAATTTAT
1 AATATTTTTTA-AAATTT-T
*
12332203 AAT-TTTTTTAAAATTTA
1 AATATTTTTTAAAATTTT
12332220 AATAT
1 AATAT
12332225 ATATATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 16 0.44
19 13 0.36
20 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTTTAAAATTTT
Found at i:12333992 original size:30 final size:30
Alignment explanation
Indices: 12333956--12334018 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12333946 ACTTAAGAAG
12333956 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
12333986 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
12334016 CAA
1 CAA
12334019 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:12335187 original size:52 final size:52
Alignment explanation
Indices: 12335124--12335229 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
12335114 TTTATATCCC
12335124 TTAAAAAATTTACCACTTGCAATTCAACTTTTAAAAAAAACATTAAAAATTA
1 TTAAAAAATTTACCACTTGCAATTCAACTTTTAAAAAAAACATTAAAAATTA
*
12335176 TTAAAAGATTTACCACTTGCAATTCAACTTTTAAAAAAAACATTAAAAATTA
1 TTAAAAAATTTACCACTTGCAATTCAACTTTTAAAAAAAACATTAAAAATTA
12335228 TT
1 TT
12335230 TTCAATAATA
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:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (52 bp):
TTAAAAAATTTACCACTTGCAATTCAACTTTTAAAAAAAACATTAAAAATTA
Found at i:12336584 original size:40 final size:40
Alignment explanation
Indices: 12336535--12336610 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
12336525 TCTTTCTGCA
12336535 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
*
12336575 AATCTCATTCCTCTCTTTCTCTCTTTCTCAGGCAAA
1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAA
12336611 TCTCATTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.18, C:0.36, G:0.08, T:0.38
Consensus pattern (40 bp):
AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
Found at i:12336613 original size:34 final size:34
Alignment explanation
Indices: 12336515--12336622 Score: 123
Period size: 40 Copynumber: 3.1 Consensus size: 34
12336505 TCATCTTCTT
*
12336515 TCTCTCTCTCTCTTTCT---GCAAATCTCATTCC
1 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
*
12336546 TCCCTTTCTCTCTTTCTCAGGCAAAGGCCAATCTCATTCC
1 TCTCTTTCTCTCTTTCTCAGGC--A----AATCTCATTCC
12336586 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
1 TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
12336620 TCT
1 TCT
12336623 TCGCAAGGTC
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
31 15 0.23
34 16 0.25
36 1 0.02
38 1 0.02
40 32 0.49
ACGTcount: A:0.15, C:0.37, G:0.06, T:0.42
Consensus pattern (34 bp):
TCTCTTTCTCTCTTTCTCAGGCAAATCTCATTCC
Found at i:12340036 original size:18 final size:18
Alignment explanation
Indices: 12340015--12340057 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
12340005 ATAATTTAAA
12340015 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
12340033 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
12340051 ATGTAAA
1 ATATAAA
12340058 AATAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:12340157 original size:19 final size:20
Alignment explanation
Indices: 12340133--12340178 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
12340123 CATCCAAACA
12340133 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
*
12340152 CCAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCATTTT
12340172 CCAGAAA
1 CCAGAAA
12340179 TCATTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:12347025 original size:15 final size:16
Alignment explanation
Indices: 12347002--12347035 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12346992 AATATTTTAA
*
12347002 AAATTATTAAAAT-AT
1 AAATGATTAAAATGAT
12347017 AAATGATTAAAATGAT
1 AAATGATTAAAATGAT
12347033 AAA
1 AAA
12347036 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
AAATGATTAAAATGAT
Found at i:12350422 original size:32 final size:32
Alignment explanation
Indices: 12350382--12350448 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
12350372 TTGATGATTG
12350382 TTGTGAGGAGTGTGCTCTTTCCGAGAGAACAA
1 TTGTGAGGAGTGTGCTCTTTCCGAGAGAACAA
12350414 TTGTGAGGAGTGTGCTCTTTCCGAGAGAACAA
1 TTGTGAGGAGTGTGCTCTTTCCGAGAGAACAA
12350446 TTG
1 TTG
12350449 GGGATGGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (32 bp):
TTGTGAGGAGTGTGCTCTTTCCGAGAGAACAA
Found at i:12352521 original size:23 final size:24
Alignment explanation
Indices: 12352477--12352522 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12352467 AATTTTTATG
12352477 TGGCATGTCTAAGAATTTGTCATT
1 TGGCATGTCTAAGAATTTGTCATT
**
12352501 TGGCATGT-TAATTATTTGTCAT
1 TGGCATGTCTAAGAATTTGTCAT
12352523 GTGTCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.46
Consensus pattern (24 bp):
TGGCATGTCTAAGAATTTGTCATT
Found at i:12360692 original size:5 final size:6
Alignment explanation
Indices: 12360678--12360722 Score: 54
Period size: 6 Copynumber: 6.8 Consensus size: 6
12360668 TCGGTACCTC
12360678 TTTTAT TTTTAT TTTTAT ATTTATAT TTTTAAT TTCTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT -TTT-TAT TTTT-AT TT-TTAT TTTTA
12360723 AAAGATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 16 0.46
7 14 0.40
8 5 0.14
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:12360706 original size:20 final size:22
Alignment explanation
Indices: 12360681--12360722 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12360671 GTACCTCTTT
12360681 TATTTTT-ATTT-TTATATTTA
1 TATTTTTAATTTCTTATATTTA
*
12360701 TATTTTTAATTTCTTATTTTTA
1 TATTTTTAATTTCTTATATTTA
12360723 AAAGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTTAATTTCTTATATTTA
Found at i:12360723 original size:14 final size:13
Alignment explanation
Indices: 12360678--12360723 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
12360668 TCGGTACCTC
12360678 TTTT-ATTTTTAT
1 TTTTAATTTTTAT
*
12360690 TTTTATATTTATAT
1 TTTTA-ATTTTTAT
12360704 TTTTAATTTCTTAT
1 TTTTAATTT-TTAT
12360718 TTTTAA
1 TTTTAA
12360724 AAGATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 21 0.72
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTAATTTTTAT
Found at i:12360949 original size:21 final size:23
Alignment explanation
Indices: 12360925--12360968 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12360915 TGAAATAATT
*
12360925 AAAA-TAAAACA-CTATTATCAA
1 AAAATTAAAACATCCATTATCAA
12360946 AAAATTAAAACATCCATTATCAA
1 AAAATTAAAACATCCATTATCAA
12360969 TATATATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATTAAAACATCCATTATCAA
Found at i:12362188 original size:21 final size:21
Alignment explanation
Indices: 12362135--12362215 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
12362125 ACCCAAGACC
*
12362135 CTGAACT-TGAAACCTTGAACA
1 CTGAACTCT-AAACCTCGAACA
* * *
12362156 CTAAATTTTAAACCTCGAACA
1 CTGAACTCTAAACCTCGAACA
*
12362177 CTGAACTCTAAACC-CAAAC-
1 CTGAACTCTAAACCTCGAACA
*
12362196 CATGAACAC-AAACCTCGAAC
1 C-TGAACTCTAAACCTCGAAC
12362216 CTCAACCCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.12
20 14 0.29
21 27 0.56
22 1 0.02
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.20
Consensus pattern (21 bp):
CTGAACTCTAAACCTCGAACA
Found at i:12363572 original size:6 final size:6
Alignment explanation
Indices: 12363563--12363602 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
12363553 CAAAATAAAA
12363563 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
12363603 AATTAAGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTCC
Found at i:12366141 original size:2 final size:2
Alignment explanation
Indices: 12366134--12366168 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12366124 TTATCCTATT
12366134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12366169 TATGTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12366305 original size:28 final size:28
Alignment explanation
Indices: 12366259--12366318 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12366249 CTAAGATGAC
* *
12366259 TATATAAAAATTTTCAATAAATAAAA-AA
1 TATATAAAAATATTAAAT-AATAAAATAA
*
12366287 TATATAAAAATATTAAATATTAAAATAA
1 TATATAAAAATATTAAATAATAAAATAA
12366315 TATA
1 TATA
12366319 ATATAAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TATATAAAAATATTAAATAATAAAATAA
Found at i:12366636 original size:17 final size:17
Alignment explanation
Indices: 12366604--12366638 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12366594 TTAATTAAGG
**
12366604 GTTAAAATAACTTAAAA
1 GTTAAAATAAAATAAAA
12366621 GTTAAAATAAAATAAAA
1 GTTAAAATAAAATAAAA
12366638 G
1 G
12366639 ATTGTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
GTTAAAATAAAATAAAA
Found at i:12366686 original size:18 final size:18
Alignment explanation
Indices: 12366663--12366700 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12366653 TTAATGTTCA
12366663 ATTTC-ATACTTAGATTTG
1 ATTTCAATACTTA-ATTTG
*
12366681 ATTTCAATATTTAATTTG
1 ATTTCAATACTTAATTTG
12366699 AT
1 AT
12366701 ATTTAGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTCAATACTTAATTTG
Found at i:12371365 original size:31 final size:31
Alignment explanation
Indices: 12371322--12371388 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
12371312 ACAAAATGGT
12371322 CACTAAACTATTCAAAAGTTTTCATTTAAGC
1 CACTAAACTATTCAAAAGTTTTCATTTAAGC
* * *
12371353 CACTGAACTATTCAAAAGTTTTTATTTAAGT
1 CACTAAACTATTCAAAAGTTTTCATTTAAGC
12371384 CACTA
1 CACTA
12371389 GGTTGTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.37
Consensus pattern (31 bp):
CACTAAACTATTCAAAAGTTTTCATTTAAGC
Found at i:12373007 original size:25 final size:25
Alignment explanation
Indices: 12372959--12373005 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12372949 AAATTTAATT
* *
12372959 TTTTCTTTTTATTTCTTTATTTTCC
1 TTTTCTTTTTACTCCTTTATTTTCC
12372984 TTTTCTTTTT-CTCCTTTATTTT
1 TTTTCTTTTTACTCCTTTATTTT
12373006 TCTCTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCTTTTTACTCCTTTATTTTCC
Found at i:12377103 original size:20 final size:18
Alignment explanation
Indices: 12377056--12377104 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
12377046 CAAGATAAAC
12377056 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
12377073 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
12377093 ATTAAATTAATA
1 ATTAAATTAATA
12377105 AAATAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:12377599 original size:19 final size:19
Alignment explanation
Indices: 12377575--12377617 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12377565 AAAATATCAT
*
12377575 ATTAATTTTAA-TTTATTTG
1 ATTAA-TTTAATTTTACTTG
12377594 ATTAATTTAATTTTACTTG
1 ATTAATTTAATTTTACTTG
12377613 ATTAA
1 ATTAA
12377618 AACAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTAATTTAATTTTACTTG
Found at i:12380964 original size:25 final size:25
Alignment explanation
Indices: 12380934--12381003 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
12380924 CCCTCTTTCA
**
12380934 AGCCATATAACAGGAAGCTCATGTG
1 AGCCATATAACAGGAAGCTCATAAG
*
12380959 AGCCATATAACGGGAAGCTCATAAG
1 AGCCATATAACAGGAAGCTCATAAG
* *
12380984 AGCCATA-ATCAAGAAGCTCA
1 AGCCATATAACAGGAAGCTCA
12381004 CGCAAGCCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 10 0.26
25 29 0.74
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (25 bp):
AGCCATATAACAGGAAGCTCATAAG
Found at i:12384388 original size:36 final size:36
Alignment explanation
Indices: 12384348--12384420 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
12384338 TAAATCATGC
12384348 CTAAAACATTAACTTATCAAATTGATCAACAACATT
1 CTAAAACATTAACTTATCAAATTGATCAACAACATT
*
12384384 CTAAAACATTGACTTATCAAATTGATCAACAACATT
1 CTAAAACATTAACTTATCAAATTGATCAACAACATT
12384420 C
1 C
12384421 ATGATACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (36 bp):
CTAAAACATTAACTTATCAAATTGATCAACAACATT
Found at i:12385089 original size:23 final size:23
Alignment explanation
Indices: 12385059--12385148 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
12385049 GGATACACGG
*
12385059 ATCCAACCAAACACACCAAAATA
1 ATCCAACCAAACACACCAGAATA
* *
12385082 ATCCAACCAAACACGCCAGAATG
1 ATCCAACCAAACACACCAGAATA
*
12385105 ATCCATCCAAACACACCAGAATA
1 ATCCAACCAAACACACCAGAATA
* *
12385128 ATCCACCCAAATACACCAGAA
1 ATCCAACCAAACACACCAGAA
12385149 CGACACTAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.49, C:0.36, G:0.06, T:0.10
Consensus pattern (23 bp):
ATCCAACCAAACACACCAGAATA
Found at i:12385346 original size:24 final size:24
Alignment explanation
Indices: 12385298--12385352 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
12385288 TATTCAATTT
12385298 TCATA-TTTCAATTCAATCACTTTC
1 TCATATTTTCAATTCAATCAC-TTC
12385322 TCATATTTTCAATTCAAATCA-TTC
1 TCATATTTTCAATTC-AATCACTTC
12385346 TCA-ATTT
1 TCATATTT
12385353 AATCACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.38
25 9 0.31
26 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (24 bp):
TCATATTTTCAATTCAATCACTTC
Found at i:12386214 original size:3 final size:3
Alignment explanation
Indices: 12386199--12386239 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
12386189 ATATATTAGT
*
12386199 TAA TAA TAT TAA TAA TAA TACA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
12386240 TTTAATTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:12386225 original size:19 final size:18
Alignment explanation
Indices: 12386201--12386236 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12386191 ATATTAGTTA
*
12386201 ATAATATTAATAATAATAC
1 ATAATAATAAT-ATAATAC
12386220 ATAATAATAATATAATA
1 ATAATAATAATATAATA
12386237 ATATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATAATATAATAC
Found at i:12388419 original size:17 final size:17
Alignment explanation
Indices: 12388373--12388419 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12388363 CTTCTGAAAA
*
12388373 AACAACT-TTTGTTTAG
1 AACAACTATTTTTTTAG
* * *
12388389 AATAATTATATTTTTAG
1 AACAACTATTTTTTTAG
12388406 AACAACTATTTTTT
1 AACAACTATTTTTT
12388420 GAGGATAGCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (17 bp):
AACAACTATTTTTTTAG
Found at i:12391408 original size:50 final size:51
Alignment explanation
Indices: 12391331--12391459 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
12391321 GACCATGGCA
12391331 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
12391382 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
12391432 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
12391460 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:12391473 original size:31 final size:31
Alignment explanation
Indices: 12391435--12391583 Score: 246
Period size: 31 Copynumber: 4.8 Consensus size: 31
12391425 ACAAATGACA
12391435 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
12391466 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
12391497 AGTGAAAAGTGGTAG-TTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-AGCTACCTGATC
12391528 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
12391559 AGTGAAAAATGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCAGCTAC
12391584 AAGTGACAAG
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 3 0.03
31 105 0.95
32 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:12391678 original size:47 final size:46
Alignment explanation
Indices: 12391608--12391730 Score: 147
Period size: 47 Copynumber: 2.7 Consensus size: 46
12391598 AAGTGATTTC
* * *
12391608 CGTATAAGACCATATCTGGGATATGGCATCTGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
12391654 CTGTATAAGGCCATATCTGGGATATGACATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
12391701 CGTGTAAGACCATAGCTGGGCTATGGCATC
1 CGTATAAGACCATATCTGGGATATGGCATC
12391731 GATATATGAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 25 0.39
47 39 0.61
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:12391753 original size:42 final size:43
Alignment explanation
Indices: 12391702--12391816 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 43
12391692 TATGTGATTC
* *
12391702 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGAGCTATGGCATCGATTATATGAAGAT
* *
12391744 GTGTAAGACCATAGCTAAGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGAGCTATGGCATCGATTATATGAAGAT
* *
12391786 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGAGCTATGGCATCGA
12391817 GAAAACGAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGAGCTATGGCATCGATTATATGAAGAT
Found at i:12393342 original size:19 final size:19
Alignment explanation
Indices: 12393256--12393355 Score: 62
Period size: 19 Copynumber: 5.3 Consensus size: 19
12393246 TTGCAAAAAA
* *
12393256 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAAAAATTAT
* **
12393275 TAAAATT-AAAAATGTTTAT
1 AAAAATTCAAAAA-AATTAT
* *
12393294 AAAAATTC-CAAAATTTAT
1 AAAAATTCAAAAAAATTAT
* ** *
12393312 ATATTTTTAAAAAAATTAT
1 AAAAATTCAAAAAAATTAT
12393331 AAAAATTCAAAAAAATCTA-
1 AAAAATTCAAAAAAAT-TAT
12393350 AAAAAT
1 AAAAAT
12393356 ATATAAAGAA
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
18 13 0.22
19 44 0.75
20 2 0.03
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAAAAATTAT
Found at i:12395569 original size:21 final size:21
Alignment explanation
Indices: 12395522--12395578 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12395512 TCAAGTTTGG
*
12395522 TTTATTTCAAT-TGAGTTTTTCT
1 TTTATTTCAATAT--GTGTTTCT
*
12395544 ATTATTTCAATATGTGTTTCT
1 TTTATTTCAATATGTGTTTCT
12395565 TTTATTTCAATATG
1 TTTATTTCAATATG
12395579 ATCAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.65
22 10 0.32
23 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTATTTCAATATGTGTTTCT
Found at i:12405472 original size:33 final size:32
Alignment explanation
Indices: 12405427--12405491 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
12405417 TTCATATTTG
* *
12405427 TTTCGTGTTTACTGTCCCGACGGACTTACTTT
1 TTTCGTGTTTACTATCCCGACAGACTTACTTT
12405459 TTTCTGTGTTTACTATCCCGACAGACTTACTTT
1 TTTC-GTGTTTACTATCCCGACAGACTTACTTT
12405492 GTTGATGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (32 bp):
TTTCGTGTTTACTATCCCGACAGACTTACTTT
Found at i:12407079 original size:17 final size:18
Alignment explanation
Indices: 12407042--12407084 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
12407032 TTTATATTTT
* *
12407042 TAAAAATATTAATTATTA
1 TAAAAATATTAAGTATGA
12407060 TAAAAATATT-AGTATGA
1 TAAAAATATTAAGTATGA
12407077 TAAAAATA
1 TAAAAATA
12407085 ATTTCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
TAAAAATATTAAGTATGA
Found at i:12409883 original size:12 final size:12
Alignment explanation
Indices: 12409831--12409883 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
12409821 GACAATTCCT
12409831 AAACCAGAGACC
1 AAACCAGAGACC
* *
12409843 AAACAAGAGGCC
1 AAACCAGAGACC
* *
12409855 AAA-GAGGAGGCC
1 AAACCA-GAGACC
12409867 AAACCAGAGACC
1 AAACCAGAGACC
12409879 AAACC
1 AAACC
12409884 GGAAACTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.49, C:0.28, G:0.23, T:0.00
Consensus pattern (12 bp):
AAACCAGAGACC
Found at i:12412508 original size:18 final size:19
Alignment explanation
Indices: 12412477--12412513 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12412467 TCAAACTATG
12412477 AAAACCTATTTTTACATTT
1 AAAACCTATTTTTACATTT
*
12412496 AAAACCT-TTTTTAGATTT
1 AAAACCTATTTTTACATTT
12412514 TCCAGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (19 bp):
AAAACCTATTTTTACATTT
Found at i:12414935 original size:32 final size:27
Alignment explanation
Indices: 12414880--12414934 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12414870 ATGCACATAC
12414880 GCACCGACGCAGGGGAGTGAAGGAAAG
1 GCACCGACGCAGGGGAGTGAAGGAAAG
12414907 GCACCGACGCAGGGGAGTGAAGGAAAG
1 GCACCGACGCAGGGGAGTGAAGGAAAG
12414934 G
1 G
12414935 AGGGTGCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.45, T:0.04
Consensus pattern (27 bp):
GCACCGACGCAGGGGAGTGAAGGAAAG
Found at i:12420798 original size:49 final size:49
Alignment explanation
Indices: 12420742--12420975 Score: 297
Period size: 49 Copynumber: 4.7 Consensus size: 49
12420732 ATCTGATACG
* * *
12420742 CATAGTAGCCTGCACTAAGTACTACACATGCGACCAATTATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACA
** ** * *
12420791 CATAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCCGGTACA
* ** *
12420841 CATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTATCGGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACA
*
12420892 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACA
* *
12420941 CGTAGTAGCCTACACTTAGTACTACACATGTGACC
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACC
12420976 TCACAATAGA
Statistics
Matches: 158, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 74 0.47
50 45 0.28
51 39 0.25
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACA
Found at i:12420917 original size:101 final size:98
Alignment explanation
Indices: 12420732--12420975 Score: 308
Period size: 100 Copynumber: 2.5 Consensus size: 98
12420722 AGCCAAAGCT
* * *
12420732 ATCTGATACGCATAGTAGCCTGCACTAAGTACTACACATGCGACCAATTATCCAGTACACATAGT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCAGTACACATAGT
*
12420797 AGCCTGCACTTAGTACTACACACATGACCTAACC
66 AGCCTGCACTTAGTACTACACACACGACC-AACC
* ** **
12420831 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTATCGGGTACACATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCAGTACACATA
** **
12420896 GTAGCCTGCACTTAGTACTACACATGCGACCAATT
64 GTAGCCTGCACTTAGTACTACACACACGACCAACC
* * * *
12420931 ATCCGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
12420976 TCACAATAGA
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
99 39 0.32
100 42 0.34
101 42 0.34
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (98 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCAGTACACATAGT
AGCCTGCACTTAGTACTACACACACGACCAACC
Found at i:12421157 original size:35 final size:35
Alignment explanation
Indices: 12421111--12421181 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
12421101 ATAGGCAGCC
12421111 ACATTTCATATGATAACAAAATATAATAAAATAAA
1 ACATTTCATATGATAACAAAATATAATAAAATAAA
12421146 ACATTTCATATGATAACAAAATATAATAAAATAAA
1 ACATTTCATATGATAACAAAATATAATAAAATAAA
12421181 A
1 A
12421182 AGAATAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (35 bp):
ACATTTCATATGATAACAAAATATAATAAAATAAA
Found at i:12425377 original size:28 final size:28
Alignment explanation
Indices: 12425309--12425387 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
12425299 GAATCATTCG
* *
12425309 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
12425337 ATATCTCACACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* * *
12425365 ATATTTCGTACACTGAGTACCAT
1 ATATTTCGCACACTAAGTGCCAT
12425388 ATTTGATTGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:12429613 original size:46 final size:45
Alignment explanation
Indices: 12429509--12429637 Score: 154
Period size: 46 Copynumber: 2.8 Consensus size: 45
12429499 AGATTTGTGT
12429509 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACGA-G
* * *
12429557 GCTAGTGTAAGACATGTCTGGGACATGCATCAGTCATATTATGA-GA-
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGCAT-TGA-GACGAG
*
12429603 GCCAGTGTAAGACATGTCTGGGACATGTATCGGCA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA
12429638 CGGTTACATG
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
45 3 0.04
46 34 0.47
47 18 0.25
48 15 0.21
49 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAG
Found at i:12433101 original size:46 final size:46
Alignment explanation
Indices: 12433049--12433223 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
12433039 TGGTTGAGCA
12433049 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
12433095 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
12433140 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
12433188 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12433224 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 17 0.16
46 48 0.44
47 26 0.24
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12433205 original size:93 final size:92
Alignment explanation
Indices: 12433046--12433215 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
12433036 GGATGGTTGA
**
12433046 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
12433111 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
* * *
12433139 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
12433204 TGAGTCGAGTTC
66 TGAGTCGAGTTC
12433216 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 7 0.10
93 65 0.90
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:12444550 original size:50 final size:50
Alignment explanation
Indices: 12444484--12444660 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
12444474 CCATGACAAC
12444484 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
12444534 AAGTGATAAGTAATAGCTTTGACTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
12444584 AAGTGATAAGTGATAACTTCGGCTACACTTATCTGATTAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
12444634 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
12444661 CTGATCAGTG
Statistics
Matches: 112, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 90 0.80
51 22 0.20
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:12444674 original size:31 final size:31
Alignment explanation
Indices: 12444636--12444722 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
12444626 ACAAATGACA
*
12444636 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
12444667 AGTGAAAAATAGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
12444698 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
12444723 AAGTGACAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:12444901 original size:49 final size:47
Alignment explanation
Indices: 12444798--12444969 Score: 187
Period size: 49 Copynumber: 3.7 Consensus size: 47
12444788 TGCTACTGTA
* * * * * *
12444798 TAAGACCATATCTAGGATATGGCATCA-GTGAGATATGTGATTCATG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
12444844 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
* *
12444893 TAAGACCATAGTTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
12444935 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
12444970 AGATGTGTAA
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.01
42 34 0.30
44 1 0.01
45 1 0.01
46 24 0.21
47 1 0.01
48 14 0.12
49 36 0.32
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:12444936 original size:42 final size:43
Alignment explanation
Indices: 12444842--12445004 Score: 179
Period size: 42 Copynumber: 3.7 Consensus size: 43
12444832 ATGTGATTCA
* *
12444842 TGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATG-TGATTACG
1 TGTAAGACCATAGTTGGGCTATGGCATCG--AT-T-ATATGAAGA-T--G
*
12444891 TGTAAGACCATAGTTGGGCTATGGCATCGA-TATATGAATATG
1 TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATG
* *
12444933 TGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATG
1 TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATG
**
12444975 TGTAAGACCATAGTTGAACTATGGCATCGA
1 TGTAAGACCATAGTTGGGCTATGGCATCGA
12445005 GAAAACGAAG
Statistics
Matches: 102, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 63 0.62
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 28 0.27
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATG
Found at i:12461226 original size:28 final size:29
Alignment explanation
Indices: 12461173--12461227 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
12461163 TCCCTACCCG
12461173 TGTGAATCACACAGCCTGGACACATGCCT
1 TGTGAATCACACAGCCTGGACACATGCCT
* *
12461202 TGTGACTCACAC-GGCTGGACACATGC
1 TGTGAATCACACAGCCTGGACACATGC
12461228 TCGTGTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (29 bp):
TGTGAATCACACAGCCTGGACACATGCCT
Found at i:12461247 original size:41 final size:41
Alignment explanation
Indices: 12461197--12461277 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
12461187 CCTGGACACA
*
12461197 TGCCTTGTGACTCACACGG-CTGGACACATGCTCGTGTCCT
1 TGCCTTGTGACTCACACGGCCTGGACACACGCTCGTGTCCT
* **
12461237 TGCCTGTGTGACTCATACGGCCTGGGTACACGCTCGTGTCC
1 TGCCT-TGTGACTCACACGGCCTGGACACACGCTCGTGTCC
12461278 CTGACCGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.14
41 13 0.37
42 17 0.49
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (41 bp):
TGCCTTGTGACTCACACGGCCTGGACACACGCTCGTGTCCT
Found at i:12461288 original size:42 final size:41
Alignment explanation
Indices: 12461197--12461288 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
12461187 CCTGGACACA
* *
12461197 TGCCT-TGTGACTCACACGGCTGGACACATGCTCGTGTCCT
1 TGCCTGTGTGACTCACACGGCTGGACACACGCTCGTGTCCC
* **
12461237 TGCCTGTGTGACTCATACGGCCTGGGTACACGCTCGTGTCCC
1 TGCCTGTGTGACTCACACGG-CTGGACACACGCTCGTGTCCC
12461279 TGACC-GTGTG
1 TG-CCTGTGTG
12461289 GTTTTATACC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 5 0.11
41 13 0.30
42 24 0.55
43 2 0.05
ACGTcount: A:0.13, C:0.32, G:0.28, T:0.27
Consensus pattern (41 bp):
TGCCTGTGTGACTCACACGGCTGGACACACGCTCGTGTCCC
Found at i:12465510 original size:11 final size:11
Alignment explanation
Indices: 12465494--12465526 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12465484 TTATATATTC
12465494 TTTAAATTTTT
1 TTTAAATTTTT
12465505 TTTAAATTTTT
1 TTTAAATTTTT
*
12465516 TAT-AATTTTT
1 TTTAAATTTTT
12465526 T
1 T
12465527 GAAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTAAATTTTT
Found at i:12465596 original size:20 final size:19
Alignment explanation
Indices: 12465545--12465601 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
12465535 AAATTTCTGG
12465545 AATTTTTATAAA-TATTTTA
1 AATTTTTA-AAATTATTTTA
*
12465564 AAATTTTAAAATTATTTTA
1 AATTTTTAAAATTATTTTA
12465583 AATTTTTGAAAATTATTTT
1 AATTTTT-AAAATTATTTT
12465602 TTAACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 3 0.09
19 20 0.59
20 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTA
Found at i:12466173 original size:22 final size:22
Alignment explanation
Indices: 12466134--12466192 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
12466124 GTTTTAAGAA
*
12466134 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
12466155 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
12466177 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
12466193 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:12466209 original size:26 final size:24
Alignment explanation
Indices: 12466163--12466222 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
12466153 ATTTGTTTTA
*
12466163 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
12466187 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
12466213 TTTTTTATTT
1 ATATTTATTT
12466223 AATAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:12466609 original size:15 final size:16
Alignment explanation
Indices: 12466589--12466618 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12466579 TTTAGAATTT
12466589 TAAATTAAAA-ATAAC
1 TAAATTAAAATATAAC
12466604 TAAATTAAAATATAA
1 TAAATTAAAATATAA
12466619 AAACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATTAAAATATAAC
Found at i:12466633 original size:22 final size:21
Alignment explanation
Indices: 12466584--12466633 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
12466574 CAATTTTTAG
*
12466584 AATTTTAAATTAAAAATAACTA
1 AATTTAAAATTAAAAATAAC-A
12466606 AA-TTAAAATATAAAAACTAA-A
1 AATTTAAAAT-TAAAAA-TAACA
12466627 AATTTAA
1 AATTTAA
12466634 TTTATGCACG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 9 0.38
22 12 0.50
23 3 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTTAAAATTAAAAATAACA
Found at i:12469267 original size:23 final size:24
Alignment explanation
Indices: 12469241--12469290 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12469231 TAATAAAATA
* *
12469241 TAAATA-TAAATAAATTTATTATT
1 TAAATAGTAAAGAAAATTATTATT
*
12469264 TAAATAGTAAAGAAAATTATTTTT
1 TAAATAGTAAAGAAAATTATTATT
12469288 TAA
1 TAA
12469291 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TAAATAGTAAAGAAAATTATTATT
Found at i:12475591 original size:3 final size:3
Alignment explanation
Indices: 12475583--12475608 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12475573 CATGAGATTT
12475583 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
12475609 GAGTTGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12475831 original size:13 final size:13
Alignment explanation
Indices: 12475809--12475840 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12475799 TTTATTTGGC
12475809 TTTTTAGGTTTTT
1 TTTTTAGGTTTTT
*
12475822 TTTTTTGGTTTTT
1 TTTTTAGGTTTTT
12475835 TTTTTA
1 TTTTTA
12475841 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.81
Consensus pattern (13 bp):
TTTTTAGGTTTTT
Found at i:12478834 original size:27 final size:27
Alignment explanation
Indices: 12478778--12478834 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
12478768 TTATGAACTT
* **
12478778 TTTATATTTTTTTAATTTTGGTTTTGA
1 TTTATATTTTTATAATTTTGGAATTGA
*
12478805 TTTATATTTTATATAATTTTTGAATT-A
1 TTTATATTTT-TATAATTTTGGAATTGA
12478832 TTT
1 TTT
12478835 GTTGATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (27 bp):
TTTATATTTTTATAATTTTGGAATTGA
Found at i:12479487 original size:14 final size:14
Alignment explanation
Indices: 12479457--12479499 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
12479447 CAAATTTAAG
*
12479457 TTTAAGATTTG-GA
1 TTTAGGATTTGAGA
12479470 TTTAGGATTTGAGA
1 TTTAGGATTTGAGA
*
12479484 TTTAGGATTTAAGA
1 TTTAGGATTTGAGA
12479498 TT
1 TT
12479500 CAAAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTGAGA
Found at i:12479493 original size:21 final size:20
Alignment explanation
Indices: 12479450--12479499 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
12479440 CTCAAATCAA
*
12479450 ATTTAAG-TTTAAGATTTGG
1 ATTTAAGATTTGAGATTTGG
*
12479469 ATTTAGGATTTGAGATTTAGG
1 ATTTAAGATTTGAGATTT-GG
12479490 ATTTAAGATT
1 ATTTAAGATT
12479500 CAAAGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTAAGATTTGAGATTTGG
Found at i:12483039 original size:31 final size:31
Alignment explanation
Indices: 12483004--12483069 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
12482994 ATTTAAGTCC
12483004 TGAACTTGACAA-TTATTCTT-ATATTGGGGTT
1 TGAACTTGACAACTT-TT-TTCATATTGGGGTT
*
12483035 TGAACTTGACAACTTTTTTCATATTGTGGTT
1 TGAACTTGACAACTTTTTTCATATTGGGGTT
12483066 TGAA
1 TGAA
12483070 TTTTTTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.06
31 28 0.88
32 2 0.06
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (31 bp):
TGAACTTGACAACTTTTTTCATATTGGGGTT
Found at i:12483322 original size:53 final size:53
Alignment explanation
Indices: 12483237--12483337 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
12483227 TTCAGGCCCC
* * * *
12483237 AATGTGGAAACAATTGTCAAGTTTAAGCCCTAACTTGGACAAATAAAAGATTT
1 AATGTGGAAACAATTGCCAAGTTCAAGACCTAACTTGGACAAAAAAAAGATTT
* * *
12483290 AATGTGGGAACAATTGCCAAGTTCATGACCTAATTTGGACAAAAAAAA
1 AATGTGGAAACAATTGCCAAGTTCAAGACCTAACTTGGACAAAAAAAA
12483338 AGTTCAGGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (53 bp):
AATGTGGAAACAATTGCCAAGTTCAAGACCTAACTTGGACAAAAAAAAGATTT
Found at i:12483688 original size:22 final size:22
Alignment explanation
Indices: 12483633--12483689 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
12483623 TTGTTGTTGT
* *
12483633 TTGTTACAATTTTGATGTTATT
1 TTGTTACAATTTTGATATTATA
* * * *
12483655 TTGCTGCCATTTTGCTATTATA
1 TTGTTACAATTTTGATATTATA
12483677 TTGTTACAATTTT
1 TTGTTACAATTTT
12483690 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.56
Consensus pattern (22 bp):
TTGTTACAATTTTGATATTATA
Found at i:12483700 original size:43 final size:44
Alignment explanation
Indices: 12483605--12483700 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
12483595 TTTTTTTCAC
* * * *
12483605 TATTGTTTTGCTGCTATTTTGTTGTTGTTTGTTACAATTTTGATG
1 TATT-TTTTGCTGCCATTTTGCTATTATTTGTTACAATTTTGATG
*
12483650 T-TATTTTGCTGCCATTTTGCTATTATATTGTTACAATTTT-AT-
1 TATTTTTTGCTGCCATTTTGCTATTAT-TTGTTACAATTTTGATG
12483692 TATTTTTTG
1 TATTTTTTG
12483701 GATATTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.02
43 27 0.63
44 14 0.33
45 1 0.02
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.60
Consensus pattern (44 bp):
TATTTTTTGCTGCCATTTTGCTATTATTTGTTACAATTTTGATG
Found at i:12485992 original size:2 final size:2
Alignment explanation
Indices: 12485985--12486010 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12485975 TCTAAGATAA
12485985 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
12486011 TTACATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12486565 original size:2 final size:2
Alignment explanation
Indices: 12486558--12486588 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12486548 CACCTAAAAT
12486558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12486589 TAATTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12487969 original size:9 final size:9
Alignment explanation
Indices: 12487955--12487995 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
12487945 TTTATGATTG
12487955 TTTTATAAT
1 TTTTATAAT
12487964 TTTTATAAGT
1 TTTTATAA-T
*
12487974 TTATATAAT
1 TTTTATAAT
*
12487983 TTTAATAAT
1 TTTTATAAT
12487992 TTTT
1 TTTT
12487996 TAAAGAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:12487980 original size:19 final size:18
Alignment explanation
Indices: 12487954--12487994 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
12487944 TTTTATGATT
*
12487954 GTTTTATAATTTTTATAA
1 GTTTTATAATTTTAATAA
12487972 GTTTATATAATTTTAATAA
1 GTTT-TATAATTTTAATAA
12487991 -TTTT
1 GTTTT
12487995 TTAAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 7 0.33
19 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
GTTTTATAATTTTAATAA
Found at i:12488054 original size:8 final size:9
Alignment explanation
Indices: 12488041--12488120 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
12488031 TTTCATTAAT
12488041 TTTTTAT-A
1 TTTTTATAA
12488049 TTTTTATAA
1 TTTTTATAA
*
12488058 TATTTATAA
1 TTTTTATAA
*
12488067 GTTTATATAAA
1 -TTTTTAT-AA
* *
12488078 TTTTAATATC
1 TTTTTATA-A
12488088 TTTTTATAA
1 TTTTTATAA
*
12488097 TTTTT-TATT
1 TTTTTATA-A
*
12488106 TTTTTATGA
1 TTTTTATAA
12488115 TTTTTA
1 TTTTTA
12488121 AGGGAAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
8 9 0.16
9 26 0.47
10 18 0.33
11 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12488098 original size:19 final size:18
Alignment explanation
Indices: 12488037--12488118 Score: 65
Period size: 19 Copynumber: 4.4 Consensus size: 18
12488027 TAGGTTTCAT
* *
12488037 TAATTTTTTATATTTTTA
1 TAATTTTATATCTTTTTA
** *
12488055 TAATATTTATAAGTTTATA
1 TAAT-TTTATATCTTTTTA
12488074 TAAATTTTAATATCTTTTTA
1 T-AATTTT-ATATCTTTTTA
* *
12488094 TAATTTTTTATTTTTTTA
1 TAATTTTATATCTTTTTA
*
12488112 TGATTTT
1 TAATTTT
12488119 TAAGGGAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 19 0.37
19 20 0.39
20 12 0.24
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (18 bp):
TAATTTTATATCTTTTTA
Found at i:12488101 original size:10 final size:10
Alignment explanation
Indices: 12488037--12488119 Score: 61
Period size: 10 Copynumber: 8.8 Consensus size: 10
12488027 TAGGTTTCAT
12488037 TAATTTTTTA
1 TAATTTTTTA
12488047 T-A-TTTTTA
1 TAATTTTTTA
*
12488055 TAA-TATTTA
1 TAATTTTTTA
* *
12488064 TAAGTTTATA
1 TAATTTTTTA
* *
12488074 TAAATTTTAA
1 TAATTTTTTA
12488084 T-ATCTTTTTA
1 TAAT-TTTTTA
12488094 TAATTTTTTA
1 TAATTTTTTA
12488104 T--TTTTTTA
1 TAATTTTTTA
*
12488112 TGATTTTT
1 TAATTTTT
12488120 AAGGGAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
8 15 0.25
9 11 0.19
10 31 0.53
11 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:12500414 original size:26 final size:26
Alignment explanation
Indices: 12500385--12500466 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
12500375 TGGTACAAAT
* * *
12500385 TGATAATGGGTTAGGGAAATGGTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
12500411 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
12500437 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
12500463 TGAT
1 TGAT
12500467 TGGCATTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:12509213 original size:6 final size:6
Alignment explanation
Indices: 12509202--12509235 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
12509192 TGTTTCACAT
12509202 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
12509236 TGCAAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:12510004 original size:26 final size:25
Alignment explanation
Indices: 12509969--12510058 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 25
12509959 GTGTTAAAGA
12509969 TTAAAGTATAAAAATTAAATGTCAAAT
1 TTAAA-TATAAAAATTAAAT-TCAAAT
* *
12509996 TTAAATATATTAAGATTAAAATTGAAAT
1 TTAAATATA--AAAATT-AAATTCAAAT
** *
12510024 AGAAGTATAAAAATTAAATCTCAAAT
1 TTAAATATAAAAATTAAAT-TCAAAT
*
12510050 TTAAGTATA
1 TTAAATATA
12510059 TTAAAAACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
25 4 0.08
26 21 0.42
27 5 0.10
28 16 0.32
29 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (25 bp):
TTAAATATAAAAATTAAATTCAAAT
Found at i:12514024 original size:18 final size:18
Alignment explanation
Indices: 12513996--12514041 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12513986 TTTTTTTGCC
12513996 AAAAATA-AAAATTGAAA-
1 AAAAATATAAAATT-AAAG
*
12514013 AAAAATTTAAAATTAAAG
1 AAAAATATAAAATTAAAG
12514031 AAAAATATAAA
1 AAAAATATAAA
12514042 GTAAAATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAAATATAAAATTAAAG
Found at i:12517028 original size:25 final size:25
Alignment explanation
Indices: 12516968--12517017 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12516958 CAGGTAAGGC
12516968 TCCTTCTCCTTCTTTCGTTCTTCAT
1 TCCTTCTCCTTCTTTCGTTCTTCAT
*
12516993 TCCTTTTCCTTCTTTCGTTCTTCAT
1 TCCTTCTCCTTCTTTCGTTCTTCAT
12517018 ATTCTCTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.04, C:0.34, G:0.04, T:0.58
Consensus pattern (25 bp):
TCCTTCTCCTTCTTTCGTTCTTCAT
Found at i:12517719 original size:2 final size:2
Alignment explanation
Indices: 12517712--12517736 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12517702 CCTTTTTAGA
12517712 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12517737 GGTAGATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12520184 original size:19 final size:19
Alignment explanation
Indices: 12520160--12520196 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12520150 TCCAAACACC
12520160 AGAAAAGTAAATCATTTTT
1 AGAAAAGTAAATCATTTTT
*
12520179 AGAAAAGTAAATTATTTT
1 AGAAAAGTAAATCATTTT
12520197 GCAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.38
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTTT
Found at i:12520206 original size:14 final size:14
Alignment explanation
Indices: 12520187--12520224 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12520177 TTAGAAAAGT
12520187 AAATTATTTTGC-AG
1 AAATTATTTT-CTAG
12520201 AAATTATTTTCTAG
1 AAATTATTTTCTAG
*
12520215 AAATCATTTT
1 AAATTATTTT
12520225 ACTGACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (14 bp):
AAATTATTTTCTAG
Found at i:12520383 original size:21 final size:21
Alignment explanation
Indices: 12520359--12520398 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12520349 AAGGAGAACC
*
12520359 GAAGCCATTTTCAATGTTGAA
1 GAAGCCATTTTCAAAGTTGAA
12520380 GAAGCCATTTTCAAAGTTG
1 GAAGCCATTTTCAAAGTTG
12520399 GCTTATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (21 bp):
GAAGCCATTTTCAAAGTTGAA
Found at i:12522920 original size:75 final size:75
Alignment explanation
Indices: 12522833--12522982 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
12522823 AAAATATTTT
12522833 CAGGTAATTTGCCAAACAACAGAAAATATTTTACACAGATTCATCCAAACACTAGAAAAGTAAAT
1 CAGGTAATTTGCCAAACAACAGAAAATATTTTACACAGATTCATCCAAACACTAGAAAAGTAAAT
12522898 CATTTTCCAG
66 CATTTTCCAG
*
12522908 CAGGTAATTTGCCAAACAACAGAAAATATTTTACACAGATTCATCCAAACATTAGAAAAGTAAAT
1 CAGGTAATTTGCCAAACAACAGAAAATATTTTACACAGATTCATCCAAACACTAGAAAAGTAAAT
12522973 CATTTTCCAG
66 CATTTTCCAG
12522983 AAATCATTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (75 bp):
CAGGTAATTTGCCAAACAACAGAAAATATTTTACACAGATTCATCCAAACACTAGAAAAGTAAAT
CATTTTCCAG
Found at i:12522966 original size:33 final size:33
Alignment explanation
Indices: 12522844--12522958 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
12522834 AGGTAATTTG
12522844 CCAAACAACAGAAAATATTTTACACAGATTCAT
1 CCAAACAACAGAAAATATTTTACACAGATTCAT
*
12522877 CCAAAC-ACTAGAAAAGTAAATCATTTTCCAGCAGGTAATT--T
1 CCAAACAAC-AG---A--AAAT-ATTTTACA-CA-G--ATTCAT
12522918 GCCAAACAACAGAAAATATTTTACACAGATTCAT
1 -CCAAACAACAGAAAATATTTTACACAGATTCAT
12522952 CCAAACA
1 CCAAACA
12522959 TTAGAAAAGT
Statistics
Matches: 65, Mismatches: 2, Indels: 30
0.67 0.02 0.31
Matches are distributed among these distances:
32 5 0.08
33 15 0.23
34 2 0.03
35 2 0.03
36 8 0.12
37 4 0.06
38 4 0.06
39 8 0.12
40 2 0.03
41 2 0.03
42 8 0.12
43 5 0.08
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (33 bp):
CCAAACAACAGAAAATATTTTACACAGATTCAT
Found at i:12523006 original size:14 final size:14
Alignment explanation
Indices: 12522969--12522999 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12522959 TTAGAAAAGT
12522969 AAATCATTTTCCAG
1 AAATCATTTTCCAG
12522983 AAATCATTTTCCAG
1 AAATCATTTTCCAG
12522997 AAA
1 AAA
12523000 ATATTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:12523814 original size:27 final size:27
Alignment explanation
Indices: 12523777--12523831 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12523767 CATGTGAATA
12523777 AAAAATATTATATTTGACAATACTCTT
1 AAAAATATTATATTTGACAATACTCTT
12523804 AAAAATATTATATTTGACAATACTCTT
1 AAAAATATTATATTTGACAATACTCTT
12523831 A
1 A
12523832 CATGTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (27 bp):
AAAAATATTATATTTGACAATACTCTT
Found at i:12530418 original size:11 final size:11
Alignment explanation
Indices: 12530402--12530434 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
12530392 CGAGATAGAA
12530402 ATAATTATTTT
1 ATAATTATTTT
12530413 ATAATTATTTT
1 ATAATTATTTT
12530424 ATAATTATTTT
1 ATAATTATTTT
12530435 GATGATTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATAATTATTTT
Done.