Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 207 of 226
Found at i:65313183 original size:15 final size:14
Alignment explanation
Indices: 65313156--65313186 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
65313146 GAAGTTCACG
65313156 AATAAAAAAAATAA
1 AATAAAAAAAATAA
65313170 AATAAAACAAAATAA
1 AATAAAA-AAAATAA
65313185 AA
1 AA
65313187 GCAAGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AATAAAAAAAATAA
Found at i:65314419 original size:18 final size:19
Alignment explanation
Indices: 65314381--65314420 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
65314371 TTTTGGGCTA
65314381 GGGTTTGCAATGGGTTATT
1 GGGTTTGCAATGGGTTATT
65314400 GGGTTTG-AATTGGG-TATT
1 GGGTTTGCAA-TGGGTTATT
65314418 GGG
1 GGG
65314421 CTAATGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (19 bp):
GGGTTTGCAATGGGTTATT
Found at i:65320389 original size:17 final size:17
Alignment explanation
Indices: 65320367--65320399 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
65320357 ATGATGAACT
65320367 TAATTA-AATAATAATAA
1 TAATTATAAT-ATAATAA
65320384 TAATTATAATATAATA
1 TAATTATAATATAATA
65320400 TTGTAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATTATAATATAATAA
Found at i:65322071 original size:2 final size:2
Alignment explanation
Indices: 65322064--65322095 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65322054 NNNNNNNNAT
65322064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65322096 AGAAAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65327857 original size:3 final size:3
Alignment explanation
Indices: 65327828--65327877 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
65327818 AACTAACACG
* * *
65327828 ATT ACT ATT ATCT -TT ATT CTT -TT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65327872 ATT ATT
1 ATT ATT
65327878 TTGCTATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.08
3 35 0.90
4 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:65330590 original size:2 final size:2
Alignment explanation
Indices: 65330583--65330621 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
65330573 AGTATTTTAA
65330583 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
65330622 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65333406 original size:3 final size:3
Alignment explanation
Indices: 65333398--65333499 Score: 150
Period size: 3 Copynumber: 34.0 Consensus size: 3
65333388 ATATAAAAAC
* * *
65333398 AAT AAT AAT ACT AAT ACT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
65333446 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT GAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65333494 AAT AAT
1 AAT AAT
65333500 TATTATTATA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65335008 original size:45 final size:45
Alignment explanation
Indices: 65334947--65335285 Score: 173
Period size: 44 Copynumber: 7.7 Consensus size: 45
65334937 TATTGGCTTT
*
65334947 AATCTGCTCCATTGCAACTTTAGGGAGATAAGATTCATCATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCATCATCTTC
* * * * *
65334992 AATCTGCCCCACTGCAA-TTTCAGGGGGATAAGATTCGT-TTATTC
1 AATCTGCTCCACTGCAACTTT-AGGGAGATAAGATTCATCATCTTC
* * * * * * *
65335036 AGTCTGCTCCGCTACAACTTTAGGGATATAAGACT-A-GAT-GT-
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCATCATCTTC
* ** * * * *
65335077 GATCTGCT-CTTTGCAACTTCAGAGAGATAAGA-TCTGTCAT-TTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTC-ATCATCTTC
* * ** * * * * *** *
65335120 AATCCGTTCTGCTACAACTTCAGGAAGATAGGATT-ATTGGCTTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCATCATCTTC
*
65335164 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCATCATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCATCATCTTC
* * * *
65335209 AATCTGC-CGCACTGC-ACTTTCAGGGGGATAAGATTCGT-TTATTC
1 AATCTGCTC-CACTGCAACTTT-AGGGAGATAAGATTCATCATCTTC
* * * * *
65335253 AGTCGGCTCCGCTACAACTTTAGGGAAATAAGA
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA
65335286 CTAGATGCGA
Statistics
Matches: 216, Mismatches: 63, Indels: 31
0.70 0.20 0.10
Matches are distributed among these distances:
39 1 0.00
40 18 0.08
41 6 0.03
42 4 0.02
43 7 0.03
44 107 0.50
45 73 0.34
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCATCATCTTC
Found at i:65335067 original size:44 final size:45
Alignment explanation
Indices: 65334947--65335068 Score: 113
Period size: 45 Copynumber: 2.7 Consensus size: 45
65334937 TATTGGCTTT
* * * *
65334947 AATCTGCTCCATTGCAACTTTAGGGAGATAAGATTCATCATCTTC
1 AATCTGCCCCACTACAACTTTAGGGAGATAAGATTCATCATATTC
* * * *
65334992 AATCTGCCCCACTGCAA-TTTCAGGGGGATAAGATTCGT-TTATTC
1 AATCTGCCCCACTACAACTTT-AGGGAGATAAGATTCATCATATTC
* * * *
65335036 AGTCTGCTCCGCTACAACTTTAGGGATATAAGA
1 AATCTGCCCCACTACAACTTTAGGGAGATAAGA
65335069 CTAGATGTGA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 30 0.48
45 33 0.52
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
AATCTGCCCCACTACAACTTTAGGGAGATAAGATTCATCATATTC
Found at i:65335157 original size:217 final size:217
Alignment explanation
Indices: 65334819--65335410 Score: 963
Period size: 217 Copynumber: 2.7 Consensus size: 217
65334809 CTACTTGCTT
* * *
65334819 AGTCTGGTCTGCTACAACTTTAGGGATGTAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
1 AGTCTGCTCCGCTACAACTTTAGGGATATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
*
65334884 AGATAGGATCTGTCATTTTAATCCGTTCCGCTACAACTTCAGGAAGATAGGATTATTGGCTTTAA
66 AGATAAGATCTGTCATTTTAATCCGTTCCGCTACAACTTCAGGAAGATAGGATTATTGGCTTTAA
* *
65334949 TCTGCTCCATTGCAACTTTAGGGAGATAAGATTCATCATCTTCAATCTGCCCCACTGCAATTTCA
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCCCCACTGCAATTTCA
65335014 GGGGGATAAGATTCGTTTATTC
196 GGGGGATAAGATTCGTTTATTC
65335036 AGTCTGCTCCGCTACAACTTTAGGGATATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
1 AGTCTGCTCCGCTACAACTTTAGGGATATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
*
65335101 AGATAAGATCTGTCATTTTAATCCGTTCTGCTACAACTTCAGGAAGATAGGATTATTGGCTTTAA
66 AGATAAGATCTGTCATTTTAATCCGTTCCGCTACAACTTCAGGAAGATAGGATTATTGGCTTTAA
* *
65335166 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCCGCACTGCACTTTCA
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCCCCACTGCAATTTCA
65335231 GGGGGATAAGATTCGTTTATTC
196 GGGGGATAAGATTCGTTTATTC
* * * * * *
65335253 AGTCGGCTCCGCTACAACTTTAGGGAAATAAGACTAGATGCGATCTGCTATCTGTAACTTCAGAG
1 AGTCTGCTCCGCTACAACTTTAGGGATATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
* * * *
65335318 AGATAAGATCTGTGATTTTAATCCGCTCCGCTACAACTTTAGGGAGATAGGATTATCT-GCTTCT
66 AGATAAGATCTGTCATTTTAATCCGTTCCGCTACAACTTCAGGAAGATAGGATTAT-TGGCTT-T
* *
65335382 -GTCTGCTCCACTGCAACTTCAGAGAGATA
129 AATCTGCTCCACTGCAACTTCAGGGAGATA
65335411 GGACTAGATG
Statistics
Matches: 351, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
217 349 0.99
218 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (217 bp):
AGTCTGCTCCGCTACAACTTTAGGGATATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAG
AGATAAGATCTGTCATTTTAATCCGTTCCGCTACAACTTCAGGAAGATAGGATTATTGGCTTTAA
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCATCATCTTCAATCTGCCCCACTGCAATTTCA
GGGGGATAAGATTCGTTTATTC
Found at i:65335426 original size:128 final size:128
Alignment explanation
Indices: 65335284--65335538 Score: 395
Period size: 128 Copynumber: 2.0 Consensus size: 128
65335274 AGGGAAATAA
*
65335284 GACTAGATGCGATCTGCTATCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCGC
1 GACTAGATGCGATCTGCTATCTGTAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTCCGC
* * *
65335349 TACAACTTTAGGGAGATAGGATTA-TCTGCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAG
66 TACAACTTCAGGGAAATAGGATTAGCCT-CTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAG
* * * *
65335412 GACTAGATGTGATCTGCTCTCTGTAACTTTAGAAAGATAAGATCTGTGATTTTAATCCGCTCTGC
1 GACTAGATGCGATCTGCTATCTGTAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTCCGC
* * *
65335477 TACAACTTCAGGGAAATAGGATTAGCCTCTTCTGTCTGTTCCACTGTAACTTCAGGGAGATA
66 TACAACTTCAGGGAAATAGGATTAGCCTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATA
65335539 AAACTTGTGG
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
128 113 0.98
129 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (128 bp):
GACTAGATGCGATCTGCTATCTGTAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTCCGC
TACAACTTCAGGGAAATAGGATTAGCCTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAG
Found at i:65335539 original size:88 final size:87
Alignment explanation
Indices: 65335446--65335720 Score: 309
Period size: 88 Copynumber: 3.1 Consensus size: 87
65335436 AACTTTAGAA
* * *
65335446 AGATAAGATCTGTGATTTTAATCCGCTCTGCTACAACTTCAGGGAAATAGGATTAGCCTCTTCTG
1 AGATAAGA-CTGTGATTTTAATCCGCTCTACTACAACTTCAGGGAGATAGGATTAGCTTCTTCTG
*
65335511 TCTGTTCCACTGTAACTTCAGGG
65 TCTGTTCCACTGCAACTTCAGGG
* * * * * *
65335534 AGATAAAACTTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGTTTAGCTTCTTCTG
1 AGATAAGAC-TGTGATTTTAATCCGCTCTACTACAACTTCAGGGAGATAGGATTAGCTTCTTCTG
*** *
65335599 TCTGTTTTGCTGCAACATCAGGG
65 TCTGTTCCACTGCAACTTCAGGG
* *
65335622 AGATAAGACT-TGCTATCTTTAATCCGCTCTACTACAACTTCAGGGAGATAGGATTTGCTTTTTC
1 AGATAAGACTGTG--AT-TTTAATCCGCTCTACTACAACTTCAGGGAGATAGGATTAGCTTCTTC
* * * * *
65335686 AGTCTGCTCCTCTACAACTGCAGGG
63 TGTCTGTTCCACTGCAACTTCAGGG
65335711 AGATAAGACT
1 AGATAAGACT
65335721 AGATGCGATA
Statistics
Matches: 153, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
86 2 0.01
87 2 0.01
88 81 0.53
89 68 0.44
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (87 bp):
AGATAAGACTGTGATTTTAATCCGCTCTACTACAACTTCAGGGAGATAGGATTAGCTTCTTCTGT
CTGTTCCACTGCAACTTCAGGG
Found at i:65335667 original size:45 final size:44
Alignment explanation
Indices: 65335611--65335720 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 44
65335601 TGTTTTGCTG
*
65335611 CAACATCAGGGAGATAAGACTTGCTATCTTT-AATCCGCT-CTACTA
1 CAACTTCAGGGAGATAAGACTTGCT-T-TTTCAATCCGCTCCT-CTA
* * * *
65335656 CAACTTCAGGGAGATAGGATTTGCTTTTTCAGTCTGCTCCTCTA
1 CAACTTCAGGGAGATAAGACTTGCTTTTTCAATCCGCTCCTCTA
*
65335700 CAACTGCAGGGAGATAAGACT
1 CAACTTCAGGGAGATAAGACT
65335721 AGATGCGATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 3 0.05
44 28 0.51
45 24 0.44
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGACTTGCTTTTTCAATCCGCTCCTCTA
Found at i:65348422 original size:3 final size:3
Alignment explanation
Indices: 65348409--65348491 Score: 112
Period size: 3 Copynumber: 27.7 Consensus size: 3
65348399 AAATTGATAT
* * *
65348409 ATA AAA ATA ATA ATA ATA CTA ATA CTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
65348457 ATA ATA ATG ATA ATA ATG ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
65348492 TATTATTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:65352038 original size:21 final size:21
Alignment explanation
Indices: 65352014--65352054 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
65352004 ATTTTTCTTG
* *
65352014 GGTCTAAGCTGATGTACTGTT
1 GGTCCAAGCTAATGTACTGTT
65352035 GGTCCAAGCTAATGTACTGT
1 GGTCCAAGCTAATGTACTGT
65352055 CAGTCCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (21 bp):
GGTCCAAGCTAATGTACTGTT
Found at i:65352060 original size:21 final size:21
Alignment explanation
Indices: 65352019--65352062 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
65352009 TCTTGGGTCT
* **
65352019 AAGCTGATGTACTGTTGGTCC
1 AAGCTAATGTACTGTCAGTCC
65352040 AAGCTAATGTACTGTCAGTCC
1 AAGCTAATGTACTGTCAGTCC
65352061 AA
1 AA
65352063 TCAATCATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
AAGCTAATGTACTGTCAGTCC
Found at i:65353582 original size:83 final size:83
Alignment explanation
Indices: 65353455--65353622 Score: 264
Period size: 83 Copynumber: 2.0 Consensus size: 83
65353445 GAGTGGGGTA
*
65353455 GGGTGGGGTGAGAATGAATGCACCAACATCCCATGGAAGTGATAATGATATTCAAAATTATACAT
1 GGGTGGGGTGAGAATGAATGCACCAACATCCCATGGAAGTGATAATGATATTCAAAATCATACAT
* *
65353520 CCATAGTGAAGTGGAGCG
66 CCATAATGAAGTAGAGCG
* * * *
65353538 GGGTGGGGTGAGAATGGATGCACGAACATCCCATGGAGGTGATAATGATTTTCAAAATCATACAT
1 GGGTGGGGTGAGAATGAATGCACCAACATCCCATGGAAGTGATAATGATATTCAAAATCATACAT
*
65353603 CTATAATGAAGTAGAGCG
66 CCATAATGAAGTAGAGCG
65353621 GG
1 GG
65353623 TTGAGGTGGA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (83 bp):
GGGTGGGGTGAGAATGAATGCACCAACATCCCATGGAAGTGATAATGATATTCAAAATCATACAT
CCATAATGAAGTAGAGCG
Found at i:65362200 original size:42 final size:41
Alignment explanation
Indices: 65362141--65362243 Score: 152
Period size: 42 Copynumber: 2.5 Consensus size: 41
65362131 GAGACATTAA
* *
65362141 ATTGGTGGATGGTGTTGTAGTGGGATCCATAGGAGTGGGAAG
1 ATTGGTGGGTGGTGTTGT-GTGGGATCCATAGGAGTAGGAAG
*
65362183 ATTGGTGGGTGGTGTTGTGATGGGGTCCATAGGAGTAGGAAG
1 ATTGGTGGGTGGTGTTGTG-TGGGATCCATAGGAGTAGGAAG
*
65362225 ATTGGTAGGTGGTGTTGTG
1 ATTGGTGGGTGGTGTTGTG
65362244 GTGTGACCCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 55 0.98
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.31
Consensus pattern (41 bp):
ATTGGTGGGTGGTGTTGTGTGGGATCCATAGGAGTAGGAAG
Found at i:65362255 original size:42 final size:41
Alignment explanation
Indices: 65362141--65362256 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 41
65362131 GAGACATTAA
* *
65362141 ATTGGTGGATGGTGTTGTAGTGGGATCCATAGGAGTGGGAAG
1 ATTGGTGG-TGGTGTTGTGGTGGGATCCATAGGAGTAGGAAG
* *
65362183 ATTGGTGGGTGGTGTTGTGATGGGGTCCATAGGAGTAGGAAG
1 ATTGGT-GGTGGTGTTGTGGTGGGATCCATAGGAGTAGGAAG
* *
65362225 ATTGGTAGGTGGTGTTGTGGTGTGACCCATAG
1 ATTGGT-GGTGGTGTTGTGGTGGGATCCATAG
65362257 AGATAGAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 62 0.97
43 2 0.03
ACGTcount: A:0.19, C:0.06, G:0.45, T:0.30
Consensus pattern (41 bp):
ATTGGTGGTGGTGTTGTGGTGGGATCCATAGGAGTAGGAAG
Found at i:65367361 original size:16 final size:17
Alignment explanation
Indices: 65367328--65367362 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
65367318 CTTCTAGGAT
*
65367328 AAAAATATTTTTAGAAC
1 AAAAATATTCTTAGAAC
65367345 AAAAATATTCTTA-AAC
1 AAAAATATTCTTAGAAC
65367361 AA
1 AA
65367363 TCTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAATATTCTTAGAAC
Found at i:65368178 original size:22 final size:21
Alignment explanation
Indices: 65368153--65368193 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
65368143 TCTTCTTCTT
65368153 CTTTGAATCCTCTGCTTTCTAG
1 CTTTGAATCCTCTG-TTTCTAG
**
65368175 CTTTGTTTCCTCTGTTTCT
1 CTTTGAATCCTCTGTTTCT
65368194 TCTTCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.07, C:0.27, G:0.12, T:0.54
Consensus pattern (21 bp):
CTTTGAATCCTCTGTTTCTAG
Found at i:65381366 original size:49 final size:48
Alignment explanation
Indices: 65381312--65381416 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
65381302 ATTACTAAAA
* * *
65381312 TTTTAAAAATGGAAAAATATTTTTTAAA-AATAAAATAAA-ATAAACAT
1 TTTTAAAAAT-GAAAAAAACTTTTAAAATAATAAAATAAATATAAACAT
*
65381359 TACTTT-AAAATGAAAAAAACTTTTAAAATAATAAAATAAATTTAAACAT
1 T--TTTAAAAATGAAAAAAACTTTTAAAATAATAAAATAAATATAAACAT
65381408 TTTTAAAAA
1 TTTTAAAAA
65381417 GTACATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
47 18 0.37
48 20 0.41
49 11 0.22
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (48 bp):
TTTTAAAAATGAAAAAAACTTTTAAAATAATAAAATAAATATAAACAT
Found at i:65381392 original size:48 final size:47
Alignment explanation
Indices: 65381307--65381415 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
65381297 CAACAATTAC
* * * *
65381307 TAAA-ATTTTAAAAATGGAAAAATATTTTTTAAAAATAAAATAAA-A
1 TAAACATTTTTAAAATGGAAAAAAACTTTTAAAAAATAAAATAAATA
*
65381352 TAAACATTACTTTAAAAT-GAAAAAAACTTTTAAAATAATAAAATAAATT
1 TAAACATT--TTTAAAATGGAAAAAAACTTTTAAAA-AATAAAATAAATA
65381401 TAAACATTTTTAAAA
1 TAAACATTTTTAAAA
65381416 AGTACATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.07
46 3 0.06
47 21 0.39
48 18 0.33
49 8 0.15
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (47 bp):
TAAACATTTTTAAAATGGAAAAAAACTTTTAAAAAATAAAATAAATA
Found at i:65385663 original size:14 final size:14
Alignment explanation
Indices: 65385646--65385672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65385636 AAAATAAACC
65385646 GTACAAAAGAACAT
1 GTACAAAAGAACAT
65385660 GTACAAAAGAACA
1 GTACAAAAGAACA
65385673 GTGACTTGAA
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:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (14 bp):
GTACAAAAGAACAT
Found at i:65398170 original size:46 final size:46
Alignment explanation
Indices: 65398070--65398343 Score: 379
Period size: 46 Copynumber: 5.9 Consensus size: 46
65398060 GAACAGCTGT
* * * * *
65398070 AACAACATTCAGACAACATTGATTTG-TACAAGAATAGACAGCATTTA
1 AACAACATTCAGACAGCA-TAATATGCTA-AAAAATGGACAGCATTTA
* *
65398117 AATAACATTCAGACAACATAATATGCTAAAAAATGGACAGCATTTA
1 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
65398163 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
1 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
* * *
65398209 AACATCATTCGGACAGCATAATATCCTAAAAAATGGACAGCATTTA
1 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
* * *
65398255 AACAACATTCGGACAGCATAATATCCTAAAAAATGGACATCATTTA
1 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
* * *
65398301 AACATCATTCGGACAGCATAATGTGCTAAAAAATGGACAGCAT
1 AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCAT
65398344 AATATCCTAA
Statistics
Matches: 210, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 191 0.91
47 19 0.09
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (46 bp):
AACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
Found at i:65398378 original size:114 final size:115
Alignment explanation
Indices: 65398219--65398457 Score: 417
Period size: 114 Copynumber: 2.1 Consensus size: 115
65398209 AACATCATTC
*
65398219 GGACAGCATAATATCCTAAAAAATGGACAGCATTTAAACAACATTCGGACAGCATAATATCCTAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCA-TTAAACAACATTCAGACAGCATAATATCCTAA
* * *
65398284 AAAATGGACATCATTTAAACATCATTCGGACAGCATAATGTGCTAAAAAAT
65 AAAATGGACATCATTTAAACATCATTCGGACAGCATAATATACCAAAAAAT
65398335 GGACAGCATAATATCCTAAAAAATGGACAGC-TTAAACAACATTCAGACAGCATAATATCCTAAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAGCATAATATCCTAAA
*
65398399 AAATGGACATCATTTAAACATCATTCGGATAGCATAATATACCAAAAAAT
66 AAATGGACATCATTTAAACATCATTCGGACAGCATAATATACCAAAAAAT
65398449 GGACAGCAT
1 GGACAGCAT
65398458 TTTGTTATCA
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 87 0.74
116 31 0.26
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (115 bp):
GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAGCATAATATCCTAAA
AAATGGACATCATTTAAACATCATTCGGACAGCATAATATACCAAAAAAT
Found at i:65398399 original size:68 final size:69
Alignment explanation
Indices: 65398265--65398407 Score: 225
Period size: 68 Copynumber: 2.1 Consensus size: 69
65398255 AACAACATTC
* * * * *
65398265 GGACAGCATAATATCCTAAAAAATGGACATCATTTAAACATCATTCGGACAGCATAATGTGCTAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCA-TTAAACAACATTCAGACAGCATAATATCCTAA
65398330 AAAAT
65 AAAAT
65398335 GGACAGCATAATATCCTAAAAAATGGACAGC-TTAAACAACATTCAGACAGCATAATATCCTAAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAGCATAATATCCTAAA
65398399 AAAT
66 AAAT
65398403 GGACA
1 GGACA
65398408 TCATTTAAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
68 38 0.56
70 30 0.44
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (69 bp):
GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAGCATAATATCCTAAA
AAAT
Found at i:65398433 original size:46 final size:46
Alignment explanation
Indices: 65398336--65398459 Score: 182
Period size: 46 Copynumber: 2.7 Consensus size: 46
65398326 CTAAAAAATG
65398336 GACAGCATAATATCCTAAAAAATGGACAGC--TTAAACAACATTCA
1 GACAGCATAATATCCTAAAAAATGGACAGCATTTAAACAACATTCA
* * *
65398380 GACAGCATAATATCCTAAAAAATGGACATCATTTAAACATCATTCG
1 GACAGCATAATATCCTAAAAAATGGACAGCATTTAAACAACATTCA
*
65398426 GATAGCATAATATACC-AAAAAATGGACAGCATTT
1 GACAGCATAATAT-CCTAAAAAATGGACAGCATTT
65398460 TGTTATCACG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
44 29 0.40
46 41 0.57
47 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (46 bp):
GACAGCATAATATCCTAAAAAATGGACAGCATTTAAACAACATTCA
Found at i:65399175 original size:42 final size:43
Alignment explanation
Indices: 65399065--65399187 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
65399055 AAAGCTTGTA
* * * *
65399065 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAT
* * * *
65399108 CAATGCCATTGTCCCAGATAGGGTCTTACACGAAATCATATA-
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAT
*
65399150 CGATGCCAATGTCCCAGACATGGTCTTACACGTAAATC
1 CAATGCCAATGTCCCAGACATGGTCTTACACG-AAATC
65399188 TCAAATCGAT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.42
43 39 0.58
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAT
Found at i:65403839 original size:3 final size:3
Alignment explanation
Indices: 65403826--65403865 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
65403816 TATATGTATC
*
65403826 ATA AAA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
65403866 TGAACTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:65414863 original size:9 final size:9
Alignment explanation
Indices: 65414851--65414876 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
65414841 AAATCTTTTC
65414851 TTTCTTTAT
1 TTTCTTTAT
65414860 TTTCTTTAT
1 TTTCTTTAT
65414869 TTTCTTTA
1 TTTCTTTA
65414877 CTTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTAT
Found at i:65429131 original size:28 final size:28
Alignment explanation
Indices: 65429092--65429153 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
65429082 TAGCCCAACC
65429092 TAAGG-GACTGCTAGAAGATGTGTTAGT
1 TAAGGTGACTGCTAGAAGATGTGTTAGT
65429119 TAAGGTGACTGCTAGAAGATGTGTTAGT
1 TAAGGTGACTGCTAGAAGATGTGTTAGT
65429147 TAAGGTG
1 TAAGGTG
65429154 CATAGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (28 bp):
TAAGGTGACTGCTAGAAGATGTGTTAGT
Found at i:65429670 original size:56 final size:56
Alignment explanation
Indices: 65429584--65429697 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
65429574 CAAAACTTTA
65429584 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
1 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
65429640 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
1 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
65429696 AA
1 AA
65429698 CTTATATTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (56 bp):
AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
Found at i:65438923 original size:25 final size:25
Alignment explanation
Indices: 65438880--65438934 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
65438870 GAGCCATCAT
* *
65438880 TGGGTAGCTCCGAAGAGCCATTTATC
1 TGGG-AGCTCCAAAGAGCCATATATC
*
65438906 TGGGAGCTCCAAATAGCCATATATC
1 TGGGAGCTCCAAAGAGCCATATATC
65438931 -GGGA
1 TGGGA
65438935 AGTTCAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (25 bp):
TGGGAGCTCCAAAGAGCCATATATC
Found at i:65439469 original size:21 final size:21
Alignment explanation
Indices: 65439444--65439487 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
65439434 TAAATTTAAC
* * *
65439444 TTAATTTAATGAAATTCATAT
1 TTAATTCAATCAAATTCAAAT
65439465 TTAATTCAATCAAATTCAAAT
1 TTAATTCAATCAAATTCAAAT
65439486 TT
1 TT
65439488 TAGGCGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATTCAATCAAATTCAAAT
Found at i:65449132 original size:9 final size:9
Alignment explanation
Indices: 65449108--65449144 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
65449098 TGAGTTTTCG
65449108 AATTCGAAT
1 AATTCGAAT
* *
65449117 AACTCGATT
1 AATTCGAAT
65449126 AATTCGAAT
1 AATTCGAAT
65449135 AATTCGAAT
1 AATTCGAAT
65449144 A
1 A
65449145 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:65450404 original size:27 final size:27
Alignment explanation
Indices: 65450373--65450447 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
65450363 CTGCATCGAG
*
65450373 ACCCCCATAGGGTAAAATGATCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
*
65450400 ACCCCCATAGGGTAAAATGGCCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
*
65450427 ACCCCCATAGTGTAAAATGAC
1 ACCCCCATAGGGTAAAATGAC
65450448 TGTTATACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACCGAAAT
Found at i:65450455 original size:27 final size:27
Alignment explanation
Indices: 65450373--65450458 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
65450363 CTGCATCGAG
65450373 ACCCCCATAGGGTAAAATGA-TCGAAAT
1 ACCCCCATAGGGTAAAATGACT-GAAAT
* *
65450400 ACCCCCATAGGGTAAAATGGCCGAAAT
1 ACCCCCATAGGGTAAAATGACTGAAAT
* **
65450427 ACCCCCATAGTGTAAAATGACTGTTAT
1 ACCCCCATAGGGTAAAATGACTGAAAT
65450454 ACCCC
1 ACCCC
65450459 TAGGAGATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACTGAAAT
Found at i:65450899 original size:54 final size:54
Alignment explanation
Indices: 65450830--65451051 Score: 317
Period size: 54 Copynumber: 4.1 Consensus size: 54
65450820 GGCGGTCAAT
65450830 AAATGATCGAAATACCCGC-ATAGGGTAAAATGA-CAGAAATACCCCTATAGGGTA
1 AAATGATCGAAATACCC-CTATAGGGTAAAATGACCA-AAATACCCCTATAGGGTA
* *
65450884 AAATGATCGAGATACCCCTATAGGGTAAAATGATCAAAATA-CCCTCATAGGGTA
1 AAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCT-ATAGGGTA
*
65450938 AAATGAT-GAAAATACCCCTATAGGGTAAAATGACCAAAATACCCCTATAAGGTA
1 AAATGATCG-AAATACCCCTATAGGGTAAAATGACCAAAATACCCCTATAGGGTA
* * * *
65450992 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAACACCCCCATAGGGTA
1 AAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCTATAGGGTA
65451046 AAATGA
1 AAATGA
65451052 CTGTTATACC
Statistics
Matches: 153, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
53 6 0.04
54 140 0.92
55 7 0.05
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (54 bp):
AAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCTATAGGGTA
Found at i:65450965 original size:81 final size:80
Alignment explanation
Indices: 65450830--65451052 Score: 320
Period size: 81 Copynumber: 2.8 Consensus size: 80
65450820 GGCGGTCAAT
* * * *
65450830 AAATGATCGAAATACCCGCATAGGGTAAAATGACAGAAATACCCCTATAGGGTAAAATGATCGAG
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACA-AAATACCCCTATAGGGTAAAATGACCAAA
*
65450895 ATACCCCTATAGGGTA
65 ATACCCCTATAAGGTA
* * *
65450911 AAATGATCAAAATACCCTCATAGGGTAAAATGATGAAAATACCCCTATAGGGTAAAATGACCAAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGA-CAAAATACCCCTATAGGGTAAAATGACCAAA
65450976 ATACCCCTATAAGGTA
65 ATACCCCTATAAGGTA
* * *
65450992 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAACACCCCCATAGGGTAAAATGAC
1 AAATGATCGAAATACCCCCATAGGGTAAAATGA-CAAAATACCCCTATAGGGTAAAATGAC
65451053 TGTTATACCT
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 126 0.99
82 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (80 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATGACAAAATACCCCTATAGGGTAAAATGACCAAAA
TACCCCTATAAGGTA
Found at i:65451052 original size:27 final size:27
Alignment explanation
Indices: 65450830--65451052 Score: 277
Period size: 27 Copynumber: 8.3 Consensus size: 27
65450820 GGCGGTCAAT
* * *
65450830 AAATGATCGAAATACCCGCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
65450857 AAATGA-CAGAAATACCCCTATAGGGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* * * *
65450884 AAATGATCGAGATACCCCTATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
65450911 AAATGATCAAAATACCCTCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
** *
65450938 AAATGATGAAAATACCCCTATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
65450965 AAATGACCAAAATACCCCTATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
65450992 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
65451019 AAATGACCAAAACACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
65451046 AAATGAC
1 AAATGAC
65451053 TGTTATACCT
Statistics
Matches: 174, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 172 0.99
28 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:65451459 original size:28 final size:28
Alignment explanation
Indices: 65451415--65451558 Score: 173
Period size: 28 Copynumber: 5.2 Consensus size: 28
65451405 ATGGCATTGT
65451415 ACTATTACTGTATTGGGCTAAGGCCCAC
1 ACTATTACTGTATTGGGCTAAGGCCCAC
* *
65451443 ACTATTACTGTACTGGGATAAGGCCCAC
1 ACTATTACTGTATTGGGCTAAGGCCCAC
* *
65451471 ACTATTACTTTATTAGGCTAAGGCCCAC
1 ACTATTACTGTATTGGGCTAAGGCCCAC
* * * **
65451499 ACTATTAATTTATTGGGCTAAAGTTCAC
1 ACTATTACTGTATTGGGCTAAGGCCCAC
* **
65451527 ACTGTTACTGTATCAGGC-AAGGCCCAC
1 ACTATTACTGTATTGGGCTAAGGCCCAC
65451554 ACTAT
1 ACTAT
65451559 ATTGATGCTG
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 10 0.10
28 86 0.90
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (28 bp):
ACTATTACTGTATTGGGCTAAGGCCCAC
Found at i:65452206 original size:21 final size:21
Alignment explanation
Indices: 65452164--65452208 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
65452154 AATTTAACTC
* * **
65452164 AATTTAATGAAATTCATTTTT
1 AATTCAATCAAATTCACATTT
65452185 AATTCAATCAAATTCACATTT
1 AATTCAATCAAATTCACATTT
65452206 AAT
1 AAT
65452209 CCTTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTCAATCAAATTCACATTT
Found at i:65452218 original size:11 final size:11
Alignment explanation
Indices: 65452202--65452226 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65452192 TCAAATTCAC
65452202 ATTTAATCCTT
1 ATTTAATCCTT
65452213 ATTTAATCCTT
1 ATTTAATCCTT
65452224 ATT
1 ATT
65452227 CCAAGCCTAG
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:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAATCCTT
Found at i:65455508 original size:109 final size:109
Alignment explanation
Indices: 65455317--65455541 Score: 335
Period size: 109 Copynumber: 2.1 Consensus size: 109
65455307 TTATACATAA
** * *
65455317 ATTCATGTATCATGAGCTGGGAATTTGATTTACACATTTCGAAGGCTACACCATGAACATTCATA
1 ATTCATGTATCATGAGCTGCCAATTCGATTAACACATTTCGAAGGCTACACCATGAACATTCATA
* *
65455382 CAGGCATATCTTGCCATGGGTTTTAACCACATGGTCTTACACAC
66 CAGACATATCTTGCCATGGGTCTTAACCACATGGTCTTACACAC
* *
65455426 ATTCATGTATCATGATCTTCCAATTCGATTAACACAGTTT-GAAGGCTACACCATGAACATTCAT
1 ATTCATGTATCATGAGCTGCCAATTCGATTAACACA-TTTCGAAGGCTACACCATGAACATTCAT
* * *
65455490 ACAGACATATCTTTCCATGGGTCTTGACCACATGGTCTTGCACAC
65 ACAGACATATCTTGCCATGGGTCTTAACCACATGGTCTTACACAC
65455535 ATTCATG
1 ATTCATG
65455542 AATTGTGATA
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 101 0.97
110 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (109 bp):
ATTCATGTATCATGAGCTGCCAATTCGATTAACACATTTCGAAGGCTACACCATGAACATTCATA
CAGACATATCTTGCCATGGGTCTTAACCACATGGTCTTACACAC
Found at i:65458090 original size:27 final size:27
Alignment explanation
Indices: 65458043--65458105 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
65458033 CCACGAGGGG
65458043 TATTCTTTCAGAGATTGCCACGAAA-GC
1 TATTCTTTCAGAGATTGCCAC-AAAGGC
* * *
65458070 TATTCTTTCATA-ATTTTCCACAAAGGT
1 TATTCTTTCAGAGA-TTGCCACAAAGGC
65458097 TATTCTTTC
1 TATTCTTTC
65458106 CTTTCGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (27 bp):
TATTCTTTCAGAGATTGCCACAAAGGC
Found at i:65467366 original size:17 final size:18
Alignment explanation
Indices: 65467346--65467380 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
65467336 AAATAACCTC
65467346 AATACCAT-AATATGCAA
1 AATACCATGAATATGCAA
*
65467363 AATATCATGAATATGCAA
1 AATACCATGAATATGCAA
65467381 CAACTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
AATACCATGAATATGCAA
Found at i:65468162 original size:23 final size:23
Alignment explanation
Indices: 65468132--65468178 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
65468122 AATTACCCTT
65468132 AATGGAACTCATTATCAGAGCCC
1 AATGGAACTCATTATCAGAGCCC
65468155 AATGGAACTCATTATCAGAGCCC
1 AATGGAACTCATTATCAGAGCCC
65468178 A
1 A
65468179 CTAACTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (23 bp):
AATGGAACTCATTATCAGAGCCC
Found at i:65470862 original size:42 final size:42
Alignment explanation
Indices: 65470803--65470905 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
65470793 CAATGCCAAC
* * *
65470803 GTCCCAGAC-GTGGTCTTACATGTAATC-AATATCGATGTC-ATT
1 GTCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATATCGA-T
65470845 GTCCCAGACAGGGTCTTACACGAAATCAAATATGATATCGAT
1 GTCCCAGACAGGGTCTTACACGAAATCAAATATGATATCGAT
*
65470887 GTCCCAGACATGGTCTTAC
1 GTCCCAGACAGGGTCTTAC
65470906 GCATAAATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
42 47 0.87
43 7 0.13
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACACGAAATCAAATATGATATCGAT
Found at i:65476672 original size:18 final size:21
Alignment explanation
Indices: 65476630--65476678 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
65476620 TTACATTTCA
*
65476630 TTTAATTTTGTTTATGAATTC
1 TTTAATTTTGTATATGAATTC
65476651 TTTAATTTT-TATA-GAATT-
1 TTTAATTTTGTATATGAATTC
65476669 TTTAGATTTT
1 TTTA-ATTTT
65476679 AAAAAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 10 0.38
20 3 0.12
21 9 0.35
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (21 bp):
TTTAATTTTGTATATGAATTC
Found at i:65478445 original size:23 final size:23
Alignment explanation
Indices: 65478419--65478494 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
65478409 ATAAGTGCCA
65478419 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
65478442 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
65478465 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
65478488 CACTGAT
1 CACTGAT
65478495 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:65478594 original size:8 final size:8
Alignment explanation
Indices: 65478581--65478609 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
65478571 ACCCGGGACT
65478581 CACTGTAA
1 CACTGTAA
65478589 CACTGTAA
1 CACTGTAA
65478597 CACTGTAA
1 CACTGTAA
65478605 CACTG
1 CACTG
65478610 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:65478740 original size:18 final size:17
Alignment explanation
Indices: 65478714--65478752 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
65478704 ATTTTCCTTC
65478714 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
65478731 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
65478749 CACA
1 CACA
65478753 ATTTATACAA
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:65493427 original size:20 final size:20
Alignment explanation
Indices: 65493398--65493435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
65493388 ATATTTGAAG
*
65493398 TATAAAAAATTATTAAAAAC
1 TATAAAAAATTAATAAAAAC
*
65493418 TATAAGAAATTAATAAAA
1 TATAAAAAATTAATAAAA
65493436 TATGATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
TATAAAAAATTAATAAAAAC
Found at i:65493934 original size:17 final size:18
Alignment explanation
Indices: 65493903--65493937 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
65493893 AAAATTGTAA
65493903 AAGAATATTAAAAATATT
1 AAGAATATTAAAAATATT
*
65493921 AAGAA-ATTATAAATATT
1 AAGAATATTAAAAATATT
65493938 TATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AAGAATATTAAAAATATT
Found at i:65494047 original size:20 final size:20
Alignment explanation
Indices: 65494018--65494056 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
65494008 ATATTTGAAG
65494018 TATAAAAAATTATTAAAAAC
1 TATAAAAAATTATTAAAAAC
*
65494038 TATAAGAAATTATTAAAAA
1 TATAAAAAATTATTAAAAA
65494057 TTCTGTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
TATAAAAAATTATTAAAAAC
Found at i:65496603 original size:18 final size:18
Alignment explanation
Indices: 65496571--65496607 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
65496561 AAATAATATT
65496571 TTGGGCTTGGGAAAAATTA
1 TTGGGCTT-GGAAAAATTA
65496590 TTGGG-TTGGAAAAATTA
1 TTGGGCTTGGAAAAATTA
65496607 T
1 T
65496608 ATGAGTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 2 0.11
19 5 0.28
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (18 bp):
TTGGGCTTGGAAAAATTA
Found at i:65496615 original size:18 final size:17
Alignment explanation
Indices: 65496580--65496616 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
65496570 TTTGGGCTTG
*
65496580 GGAAAAATTATTGGGTT
1 GGAAAAATTATTGAGTT
65496597 GGAAAAATTATATGAGTT
1 GGAAAAATTAT-TGAGTT
65496615 GG
1 GG
65496617 TTTGAGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (17 bp):
GGAAAAATTATTGAGTT
Found at i:65500931 original size:57 final size:57
Alignment explanation
Indices: 65500870--65501170 Score: 300
Period size: 57 Copynumber: 5.3 Consensus size: 57
65500860 TAAAATAACT
* * * * * *
65500870 TTCCACATATAAGATAATATTGACGGATTTCCTACATATAAGATAGTCCTGGTGGAC
1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC
* * * * * *
65500927 TTCCACATATACGATAGTCTTGGCGGACTT-CTCGCATAAAAGATAGTCTTGGCGAAC
1 TTCCACATTTACGATAGTCTTGACGGACTTCCT-ACATATAAGATAGTCCTGGCGGAC
* * * *
65500984 TTCCACATTTACGATAGTCCTGATGGACTT-CTAACATATAAGATAGTCCTCGCAGAC
1 TTCCACATTTACGATAGTCTTGACGGACTTCCT-ACATATAAGATAGTCCTGGCGGAC
* ** * * *
65501041 TTCCACATTTACGATAGTGTTGACAAACTTCCTATATATAAGATAGTCCTAGTGGAC
1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC
* * * ** * * *
65501098 TTCCACATTTATGATAGCCCTGACGGGTTTCCCACATATAAGATAGTCTTGGCGAAC
1 TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC
65501155 TTCCACATTTACGATA
1 TTCCACATTTACGATA
65501171 ATGCCATGAC
Statistics
Matches: 197, Mismatches: 45, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
56 2 0.01
57 193 0.98
58 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (57 bp):
TTCCACATTTACGATAGTCTTGACGGACTTCCTACATATAAGATAGTCCTGGCGGAC
Found at i:65503682 original size:50 final size:50
Alignment explanation
Indices: 65503607--65503799 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
65503597 ATTTGGGTAA
* **
65503607 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
65503657 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
65503707 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
65503757 AGTACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
65503800 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:65505956 original size:20 final size:20
Alignment explanation
Indices: 65505905--65505956 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
65505895 AAATCATTGC
65505905 AATATATGTAAAAATAATTT
1 AATATATGTAAAAATAATTT
* *
65505925 AA-A-ATATAAAAAT-TTATT
1 AATATATGTAAAAATAAT-TT
65505943 AATATATGTAAAAA
1 AATATATGTAAAAA
65505957 CAACTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 2 0.08
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATATATGTAAAAATAATTT
Found at i:65506071 original size:20 final size:20
Alignment explanation
Indices: 65506046--65506085 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
65506036 AATATTTTCC
*
65506046 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
65506066 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
65506086 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:65506087 original size:34 final size:35
Alignment explanation
Indices: 65506034--65506100 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
65506024 CAAACACCAG
*
65506034 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
65506069 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
65506101 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:65507720 original size:21 final size:21
Alignment explanation
Indices: 65507694--65507734 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
65507684 GAATTACAAA
65507694 AAAAAAATCAAAATAATTTTC
1 AAAAAAATCAAAATAATTTTC
*
65507715 AAAAAATTCAAAATAATTTT
1 AAAAAAATCAAAATAATTTT
65507735 TAAATCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAAATCAAAATAATTTTC
Found at i:65507776 original size:39 final size:38
Alignment explanation
Indices: 65507698--65507777 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
65507688 TACAAAAAAA
*
65507698 AAATCAAAATAATTTTCAAAAAATTCAAAATAATTTTT
1 AAATCAAAATAATTTTCAAAAAATTCAAAATAATATTT
*
65507736 AAATCTAAAAT-ATTTAT-AAAAAATTCAAAACTTATATTT
1 AAATC-AAAATAATTT-TCAAAAAATTCAAAA-TAATATTT
65507775 AAA
1 AAA
65507778 AAATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
38 22 0.59
39 15 0.41
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (38 bp):
AAATCAAAATAATTTTCAAAAAATTCAAAATAATATTT
Found at i:65512351 original size:19 final size:19
Alignment explanation
Indices: 65512327--65512366 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
65512317 TTTCGAGGAA
65512327 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
65512346 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
65512365 AT
1 AT
65512367 ATACAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGCAATCTTAGATATGAT
Found at i:65512373 original size:21 final size:19
Alignment explanation
Indices: 65512330--65512379 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
65512320 CGAGGAAATG
*
65512330 CAATCTTAGATATGATATG
1 CAATCTTAGATATGATATA
65512349 CAATCTTAGATATGATATATA
1 CAATCTTAGATATG--ATATA
65512370 CAATCTTAGA
1 CAATCTTAGA
65512380 AGATATGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (19 bp):
CAATCTTAGATATGATATA
Found at i:65512384 original size:19 final size:19
Alignment explanation
Indices: 65512330--65512385 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
65512320 CGAGGAAATG
* *
65512330 CAATCTTAG-ATATGATATG
1 CAATCTTAGAAGAT-ATATA
65512349 CAATCTTAGATATGATATATA
1 CAATCTTAGA-A-GATATATA
65512370 CAATCTTAGAAGATAT
1 CAATCTTAGAAGATAT
65512386 GATTTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 14 0.44
20 1 0.03
21 15 0.47
22 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
CAATCTTAGAAGATATATA
Found at i:65512603 original size:19 final size:21
Alignment explanation
Indices: 65512579--65512617 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
65512569 CTGTTTTCTT
*
65512579 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
65512598 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
65512618 TTTAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:65519158 original size:44 final size:44
Alignment explanation
Indices: 65518980--65520088 Score: 172
Period size: 44 Copynumber: 25.2 Consensus size: 44
65518970 AGGATCGTAG
* *
65518980 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAGGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * * *
65519024 ATCTTATTTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTA-TCTCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * * * *
65519068 GCCTTGTTTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTG-TAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* *
65519112 ATCTTATCTCCCTAAGTAGTAGTGGAGAAGATTGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * *
65519156 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * * * * * * *
65519200 GCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* ** * * **
65519244 ATTTTATCTTTCTAAGCAGTAGTGGAGAAGATCGAAGACGGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * *
65519288 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * ** * * * *
65519332 GCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGCTAAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* ** * *
65519376 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * * *
65519420 ACCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * * * * * * * *
65519464 GCCTTGTTTCCTTGAGCAGCAGCGGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* ** *
65519508 ATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * * *
65519552 ATCTTATCTTTCC--AGGA-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
* * * * * * * * *
65519596 ACCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* * * ** * *
65519640 ATCTGATCTCCCTAAGCAGTAATGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * * * *
65519684 ATCTTATTTTTCC-AAG-A-TAATGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTA-TCTCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * ** * * * *
65519728 GCCTTGTCTCCCTAAGCAGCAGCAGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* **
65519772 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
* * * *
65519816 ATCTTATCTTTCC-AAG-A-TAGTGGGAATTAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * * ** * * * * *
65519860 GCCTTGTCTCCATGAGCAGCAACGGAGTAGGTTAAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* * * *
65519904 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
** * *
65519948 ATCTTATCTTTCTAAG-A-TAGTGGGAAGTAGATTTAAG-CCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGTAGATTGAAGACGA-CAA
** * * * * * * * * *
65519992 GCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA-CGACAA
* *
65520036 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
65520080 ATCTTATCT
1 ATCTTATCT
65520089 TTCCAAGATA
Statistics
Matches: 715, Mismatches: 272, Indels: 156
0.63 0.24 0.14
Matches are distributed among these distances:
42 32 0.04
43 68 0.10
44 551 0.77
45 48 0.07
46 16 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGACAA
Found at i:65520180 original size:132 final size:132
Alignment explanation
Indices: 65518934--65520124 Score: 1869
Period size: 132 Copynumber: 9.0 Consensus size: 132
65518924 ATGAAACACT
* * *
65518934 AAGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAGGATCGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * *
65518999 TAGTGGAGTAGATCGAGGACGACAAATCTTATTTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519064 CC
131 CC
* * * * *
65519066 AAGCCTTGTTTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAAATCTTATCTCCCTAAGTAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
65519131 TAGTGGAGAAGATTGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519196 CC
131 CC
* * **
65519198 AAGCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAGATTTTATCTTTCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
65519263 TAGTGGAGAAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519328 CC
131 CC
* * *
65519330 AAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * *
65519395 TAGTGGAGCAGATCAAATATGACAAACCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519460 CC
131 CC
* *
65519462 AAGCCTTGTTTCCTTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
65519527 TAGTGGAGAAGATCAAAGACGGCAAATCTTATCTTTCCAGGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519592 CC
131 CC
* *
65519594 AAACCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTGATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * *
65519659 TAATGGAGCAGATCAAAGATGGCAAATCTTATTTTTCCAAGATAATGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519724 CC
131 CC
* *
65519726 AAGCCTTGTCTCCCTAAGCAGCAGCAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * **
65519791 TAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAATTAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519856 CC
131 CC
* * * *
65519858 AAGCCTTGTCTCCATGAGCAGCAACGGAGTAGGTTAAAGATTGTAGATCTTATCTCTCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
65519923 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCTAAGATAGTGGGAAGTAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
65519988 CC
131 CC
*
65519990 AAGCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
65520055 TAGTGGAGTAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCA
66 TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
65520120 AC
131 CC
65520122 AAG
1 AAG
65520125 TCTTATCCTC
Statistics
Matches: 971, Mismatches: 88, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 971 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:65520437 original size:19 final size:19
Alignment explanation
Indices: 65520409--65520483 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
65520399 AATTTTCGAG
65520409 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
65520428 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
65520447 GATATATGCAATCTTAGATAT
1 GATATA--CAATCTTAGATAT
*
65520468 GATATATAATCTTAGA
1 GATATACAATCTTAGA
65520484 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 32 0.63
21 19 0.37
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:65520516 original size:22 final size:23
Alignment explanation
Indices: 65520474--65520516 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
65520464 ATATGATATA
*
65520474 TAATCTTAGAAGATATGATTTTG
1 TAATCTTAGAAGATATAATTTTG
*
65520497 TAATCTTAG-AGATTTAATTT
1 TAATCTTAGAAGATATAATTT
65520517 GTAGATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
TAATCTTAGAAGATATAATTTTG
Found at i:65520707 original size:19 final size:21
Alignment explanation
Indices: 65520683--65520721 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
65520673 CTGTTTTCTT
*
65520683 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
65520702 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
65520722 TTTAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:65520952 original size:3 final size:3
Alignment explanation
Indices: 65520944--65520989 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
65520934 ATTAATTTTG
65520944 TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
65520989 T
1 T
65520990 ACCTACATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:65520986 original size:24 final size:23
Alignment explanation
Indices: 65520944--65520990 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
65520934 ATTAATTTTG
65520944 TTATTATTATTATTATTATTATA
1 TTATTATTATTATTATTATTATA
65520967 TTATATATTATTATTATTATTATA
1 TTAT-TATTATTATTATTATTATA
65520991 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTATTATTATTATTATTATA
Found at i:65532881 original size:7 final size:7
Alignment explanation
Indices: 65532862--65532905 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
65532852 ACTAACACAA
65532862 TTGTAATT
1 TTGTAA-T
65532870 TTGTAAT
1 TTGTAAT
65532877 TTGTAA-
1 TTGTAAT
65532883 TTGTAATT
1 TTGTAA-T
65532891 TTGTAAT
1 TTGTAAT
65532898 TTGTAAT
1 TTGTAAT
65532905 T
1 T
65532906 GTGATTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.18
7 16 0.47
8 12 0.35
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TTGTAAT
Found at i:65532885 original size:21 final size:21
Alignment explanation
Indices: 65532860--65532913 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
65532850 CAACTAACAC
65532860 AATTGTAATTTTGTAATTTGT
1 AATTGTAATTTTGTAATTTGT
65532881 AATTGTAATTTTGTAATTTGT
1 AATTGTAATTTTGTAATTTGT
*
65532902 AATTGTGATTTT
1 AATTGTAATTTT
65532914 AGGAACTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
AATTGTAATTTTGTAATTTGT
Found at i:65533103 original size:83 final size:83
Alignment explanation
Indices: 65533005--65533170 Score: 269
Period size: 83 Copynumber: 2.0 Consensus size: 83
65532995 AAGAATAAAG
* * * * *
65533005 AGATAGGAAAGCAAAAGAGAATTGTGTAATTTATTTATAATGAGAATATGCTTTTCCTAAGTTTA
1 AGATAGAAAAGCAAAAGAGAACTGTGTAATTTATTTATAATGAGAATATGCTTCTCCAAAGTCTA
65533070 TATTTATAAACATAAGAA
66 TATTTATAAACATAAGAA
65533088 AGATAGAAAAGCAAAAGAGAACTGTGTAATTTATTTATAATGAGAATATGCTTCTCCAAAGTCTA
1 AGATAGAAAAGCAAAAGAGAACTGTGTAATTTATTTATAATGAGAATATGCTTCTCCAAAGTCTA
* *
65533153 TATTTATAGATATAAGAA
66 TATTTATAAACATAAGAA
65533171 GTATATATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (83 bp):
AGATAGAAAAGCAAAAGAGAACTGTGTAATTTATTTATAATGAGAATATGCTTCTCCAAAGTCTA
TATTTATAAACATAAGAA
Found at i:65537533 original size:38 final size:39
Alignment explanation
Indices: 65537477--65537550 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
65537467 TATTATTTCA
*
65537477 CATATATATAAATTAATAAATATAATCATACAATTCAAC
1 CATATATATAAATTAATAAATATAATCATAAAATTCAAC
65537516 CATA-ATATAAATTAATAAATATAATCATAAAATTC
1 CATATATATAAATTAATAAATATAATCATAAAATTC
65537551 CATATGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (39 bp):
CATATATATAAATTAATAAATATAATCATAAAATTCAAC
Found at i:65554937 original size:133 final size:132
Alignment explanation
Indices: 65554718--65554968 Score: 387
Period size: 133 Copynumber: 1.9 Consensus size: 132
65554708 AAACGATTGG
65554718 ATTTATTTAAGAAACTAAAGTCTATGGGTAAGCCCCTAGGCAAAGGCCAAAAGTTTGAAATATTG
1 ATTTATTTAAGAAACTAAAGTCTATGGGTAAGCCCCTAGGCAAAGGCCAAAAGTTTGAAATATTG
* *
65554783 TCTAGAAGAATAGAGATTAAGGAATTAGTTTTAAGTGTTCAACGTTAGAATTTTTGAAAATGATT
66 TCTAGAAGAATAAAGATTAAGGAATTAGTTTTAAGTGTTCAACGGTAGAATTTTTGAAAATGATT
65554848 AA
131 AA
* * * ** *
65554850 ATTTATTTAAGAAATTGAAGTCTATGGGTAAGCCCCTCGGTGAA-GCCTTGAAAGTTTGAAATAT
1 ATTTATTTAAGAAACTAAAGTCTATGGGTAAGCCCCTAGGCAAAGGCC--AAAAGTTTGAAATAT
* *
65554914 TGTCTAGAAGAATAAAGCTTAAGGAATTAGTTTTAAGTGTTCAACGGTAGGATTT
64 TGTCTAGAAGAATAAAGATTAAGGAATTAGTTTTAAGTGTTCAACGGTAGAATTT
65554969 GACTAAGTGT
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
131 3 0.03
132 39 0.36
133 65 0.61
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (132 bp):
ATTTATTTAAGAAACTAAAGTCTATGGGTAAGCCCCTAGGCAAAGGCCAAAAGTTTGAAATATTG
TCTAGAAGAATAAAGATTAAGGAATTAGTTTTAAGTGTTCAACGGTAGAATTTTTGAAAATGATT
AA
Found at i:65556594 original size:27 final size:29
Alignment explanation
Indices: 65556539--65556610 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 29
65556529 ATCGGTAAAT
* * *
65556539 AATGACCTTTGTGGCCTTTTTCTGTTAAAA-
1 AATG-CCTTTATGG-CTATTTCTGCTAAAAG
65556569 AA-GCCTTTATGGCTATTTCTGCTAAAAG
1 AATGCCTTTATGGCTATTTCTGCTAAAAG
*
65556597 AATGCCTTTGTGGC
1 AATGCCTTTATGGC
65556611 AATTAGTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 13 0.36
28 10 0.28
29 11 0.31
30 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (29 bp):
AATGCCTTTATGGCTATTTCTGCTAAAAG
Found at i:65556763 original size:28 final size:27
Alignment explanation
Indices: 65556732--65556821 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 27
65556722 AGTCTCTAGA
*
65556732 AAAGAACGCCTTTATGGCTGACTCTATT
1 AAAGAA-GCCTTTGTGGCTGACTCTATT
*
65556760 AAAGAAAGCATTTGTGGCTGACTCTATT
1 AAAG-AAGCCTTTGTGGCTGACTCTATT
* *
65556788 AAAGGAAGCCTTTGTGGTTGACTCTTTT
1 AAA-GAAGCCTTTGTGGCTGACTCTATT
65556816 AAAGAA
1 AAAGAA
65556822 ACCCTCGCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
27 3 0.05
28 49 0.89
29 3 0.05
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
AAAGAAGCCTTTGTGGCTGACTCTATT
Found at i:65573224 original size:17 final size:17
Alignment explanation
Indices: 65573202--65573234 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
65573192 TCCCAGGTTT
65573202 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
65573219 TGATACCCATATCTTT
1 TGATACCCATATCTTT
65573235 AACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:65590390 original size:22 final size:22
Alignment explanation
Indices: 65590362--65590426 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
65590352 TTTATTGTTC
65590362 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
65590384 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
65590406 AGCCATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
65590427 AATCGAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:65594584 original size:29 final size:29
Alignment explanation
Indices: 65594546--65594606 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
65594536 AAGTAATTAA
* *
65594546 TATTATATATGAAAGATATAAACTTATAT
1 TATTATATATAAAAGATATAAACTTAAAT
*
65594575 TATTATATATAAAATATATAAACTTAAAT
1 TATTATATATAAAAGATATAAACTTAAAT
65594604 TAT
1 TAT
65594607 AATAAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
TATTATATATAAAAGATATAAACTTAAAT
Found at i:65595099 original size:22 final size:21
Alignment explanation
Indices: 65595074--65595128 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
65595064 AAAAATCTTT
65595074 AAATTTGAAAAAAAAATACAAA
1 AAATTT-AAAAAAAAATACAAA
* * *
65595096 AAATTATAAAAAAAATTAGAGA
1 AAATT-TAAAAAAAAATACAAA
*
65595118 AAATTTTAAAA
1 AAATTTAAAAA
65595129 TATGTATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.18
22 22 0.79
23 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATTTAAAAAAAAATACAAA
Found at i:65597941 original size:25 final size:25
Alignment explanation
Indices: 65597913--65597961 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
65597903 AATACTTATA
*
65597913 TGAG-CATGTAAACGGGAAGCTCATG
1 TGAGTCATGT-AACGGAAAGCTCATG
65597938 TGAGTCATGTAACGGAAAGCTCAT
1 TGAGTCATGTAACGGAAAGCTCAT
65597962 AAGAGCTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (25 bp):
TGAGTCATGTAACGGAAAGCTCATG
Found at i:65598049 original size:25 final size:25
Alignment explanation
Indices: 65598021--65598098 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
65598011 AGAACCGTTA
* *
65598021 ATCAGGAAGCTCATGACAGCCAGAT
1 ATCAGGAAGCTCATGAGAGCCAAAT
*
65598046 ATCAGGAAGCTCGTGAGAGCCAAAT
1 ATCAGGAAGCTCATGAGAGCCAAAT
* * *
65598071 AACAGGAAGCTCAAGAGAGCCATAT
1 ATCAGGAAGCTCATGAGAGCCAAAT
65598096 ATC
1 ATC
65598099 GATAAATACA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.15
Consensus pattern (25 bp):
ATCAGGAAGCTCATGAGAGCCAAAT
Found at i:65598253 original size:25 final size:25
Alignment explanation
Indices: 65598205--65598253 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
65598195 TCCGAGCTAT
* * **
65598205 ATATAACGGGAAGCTCATGTGAGTC
1 ATATAACAGAAAGCTCATAAGAGTC
65598230 ATATAACAGAAAGCTCATAAGAGT
1 ATATAACAGAAAGCTCATAAGAGT
65598254 TGTAATCAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (25 bp):
ATATAACAGAAAGCTCATAAGAGTC
Found at i:65598437 original size:25 final size:25
Alignment explanation
Indices: 65598313--65598451 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
65598303 GTTAATCAGA
* *
65598313 AAGCTCATGAGAGCCAGATATCGAG
1 AAGCTCATGAGAGCCAAATATCGGG
* * *
65598338 AAGCTCGTGAGAGCCAAATAACAGG
1 AAGCTCATGAGAGCCAAATATCGGG
* *
65598363 AAGCTCAAGAGAGCCATATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * * *
65598388 AAGTTCATAAGAGCTAAATAACGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * *
65598413 CAGATCATGAGAGCCATATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
*
65598438 ACA-CTCATAAGAGC
1 A-AGCTCATGAGAGC
65598452 TGTGGTGAGT
Statistics
Matches: 88, Mismatches: 25, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
25 87 0.99
26 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAAATATCGGG
Found at i:65598452 original size:50 final size:50
Alignment explanation
Indices: 65598317--65598452 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 50
65598307 ATCAGAAAGC
* * * * * *
65598317 TCATGAGAGCCAGATATCGAGAAGCTCGTGAGAGCCAAATAACAGGAAGC
1 TCATGAGAGCCATATATCGGGAAGCTCATAAGAGCTAAATAACAGGAAGA
* * * *
65598367 TCAAGAGAGCCATATATCGGGAAGTTCATAAGAGCTAAATAACGGGCAGA
1 TCATGAGAGCCATATATCGGGAAGCTCATAAGAGCTAAATAACAGGAAGA
65598417 TCATGAGAGCCATATATCGGGACA-CTCATAAGAGCT
1 TCATGAGAGCCATATATCGGGA-AGCTCATAAGAGCT
65598453 GTGGTGAGTC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 72 0.99
51 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (50 bp):
TCATGAGAGCCATATATCGGGAAGCTCATAAGAGCTAAATAACAGGAAGA
Found at i:65600861 original size:25 final size:25
Alignment explanation
Indices: 65600833--65600906 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
65600823 TAAACTCCTC
*
65600833 CGAGCTGAATAACGATAAGCTCTTT
1 CGAGCTGAATAACGATAAGCTCATT
* *
65600858 CGAGCTGAATAACGGTAAGTTCATT
1 CGAGCTGAATAACGATAAGCTCATT
* *
65600883 CGAGCTGAATATCAATAAGCTCAT
1 CGAGCTGAATAACGATAAGCTCAT
65600907 ACAAGATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (25 bp):
CGAGCTGAATAACGATAAGCTCATT
Found at i:65600862 original size:49 final size:50
Alignment explanation
Indices: 65600802--65600904 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 50
65600792 GAATCGGTAT
* *
65600802 GCTCTTACGAGCT--ATAAACGGTAAACTCCTCCGAGCTGAATAACGATAA
1 GCTCTTACGAGCTGAAT-AACGGTAAACTCATCCGAGCTGAATAACAATAA
* ** * *
65600851 GCTCTTTCGAGCTGAATAACGGTAAGTTCATTCGAGCTGAATATCAATAA
1 GCTCTTACGAGCTGAATAACGGTAAACTCATCCGAGCTGAATAACAATAA
65600901 GCTC
1 GCTC
65600905 ATACAAGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 12 0.27
50 31 0.69
51 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (50 bp):
GCTCTTACGAGCTGAATAACGGTAAACTCATCCGAGCTGAATAACAATAA
Found at i:65604726 original size:25 final size:25
Alignment explanation
Indices: 65604671--65604740 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
65604661 AGCTATAAAT
* *
65604671 GGTAAGCTCCTCCGAGCTGAATAAC
1 GGTAAGCTCTTTCGAGCTGAATAAC
**
65604696 AATAAGCTCTTTCGAGCTGAATAAC
1 GGTAAGCTCTTTCGAGCTGAATAAC
*
65604721 GGTAAGTTCATTT-GAGCTGA
1 GGTAAGCTC-TTTCGAGCTGA
65604741 GTATCAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 34 0.92
26 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCTTTCGAGCTGAATAAC
Found at i:65611565 original size:58 final size:58
Alignment explanation
Indices: 65611501--65611629 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 58
65611491 GAATGAATAG
* *
65611501 AAATAGAGAAATGAAAAAT-ATTTAGGGAATG-ATTATGATTTTCTCCAAATGAAAATGA
1 AAATAGAGAAATGAAAAATCATTT-GGAAATGAATT-TGATTTTCTCAAAATGAAAATGA
* *
65611559 AAATAGAGAAAATG--GAATCATTTGGAAATGAATTTGATTTTCTCAAAATGGAAATGA
1 AAATAGAG-AAATGAAAAATCATTTGGAAATGAATTTGATTTTCTCAAAATGAAAATGA
65611616 AAAT-GAGAAATGAA
1 AAATAGAGAAATGAA
65611630 TTCATTTAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
55 5 0.08
56 3 0.05
57 34 0.55
58 15 0.24
59 5 0.08
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.28
Consensus pattern (58 bp):
AAATAGAGAAATGAAAAATCATTTGGAAATGAATTTGATTTTCTCAAAATGAAAATGA
Found at i:65611598 original size:57 final size:55
Alignment explanation
Indices: 65611528--65611642 Score: 153
Period size: 57 Copynumber: 2.1 Consensus size: 55
65611518 ATATTTAGGG
* *
65611528 AATGATTATGATTTTCTCCAAATGAAAATGAAAATAGAGAAAATGGAA-TCATTTGGA
1 AATGATTATGATTTTCTCAAAATGAAAATGAAAAT-GAG-AAAT-GAATTCATTTAGA
*
65611585 AATGAATT-TGATTTTCTCAAAATGGAAATGAAAATGAGAAATGAATTCATTTAGA
1 AATG-ATTATGATTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGA
65611640 AAT
1 AAT
65611643 AGAAAATGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
54 3 0.06
55 15 0.28
56 3 0.06
57 29 0.55
58 3 0.06
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (55 bp):
AATGATTATGATTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGA
Found at i:65611657 original size:55 final size:57
Alignment explanation
Indices: 65611535--65611661 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 57
65611525 GGGAATGATT
* * * *
65611535 ATGATTTTCTCCAAATGAAAATGAAAATAGAGAAAATGGAATCATTTGGAAATGAAT
1 ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAATCATTTAGAAATGAAA
* * *
65611592 TTGATTTTCTCAAAATGGAAATGAAAAT-GAG-AAAT-GAATTCATTTAGAAATAGAAA
1 ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAA-TCATTTAGAAAT-GAAA
65611648 ATGA-ATTCTCAAAA
1 ATGATATTCTCAAAA
65611662 ATAATCAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
54 3 0.05
55 24 0.39
56 9 0.15
57 25 0.41
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (57 bp):
ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAATCATTTAGAAATGAAA
Found at i:65612837 original size:6 final size:6
Alignment explanation
Indices: 65612821--65612871 Score: 75
Period size: 6 Copynumber: 8.3 Consensus size: 6
65612811 TTTCTTTCCA
* *
65612821 TTCTCTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTC TTATTT TTCTTT
1 TTCT-TT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
65612870 TT
1 TT
65612872 ACTTGTTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 36 0.90
7 4 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:65617843 original size:39 final size:39
Alignment explanation
Indices: 65617789--65617867 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
65617779 TTCCGGTGAT
*
65617789 CCCTTGGCGAATGACGCGAGTGTTTTTGTCTACGAAAAC
1 CCCTTGGCAAATGACGCGAGTGTTTTTGTCTACGAAAAC
65617828 CCCTTGGCAAATGACGCGAGTGTTTTTGTCTACGAAAAC
1 CCCTTGGCAAATGACGCGAGTGTTTTTGTCTACGAAAAC
65617867 C
1 C
65617868 ACCGGTTGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (39 bp):
CCCTTGGCAAATGACGCGAGTGTTTTTGTCTACGAAAAC
Found at i:65619557 original size:87 final size:87
Alignment explanation
Indices: 65619411--65619592 Score: 337
Period size: 87 Copynumber: 2.1 Consensus size: 87
65619401 CAACAAATGA
65619411 TAAAATCATCAATGCATAAAAACTTATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
1 TAAAATCATCAATGCATAAAAACTTATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
65619476 TTAAACTTAAACCAGATAAGTG
66 TTAAACTTAAACCAGATAAGTG
* *
65619498 TAAAATCATCAATGCGTAAAAACTTATAAAATATAGAACTTGACTGATGCATTTTAACAAATTGT
1 TAAAATCATCAATGCATAAAAACTTATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
65619563 TTAAACTTAAACCAGATAAGTG
66 TTAAACTTAAACCAGATAAGTG
*
65619585 TAATATCA
1 TAAAATCA
65619593 ATGTTAGTCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (87 bp):
TAAAATCATCAATGCATAAAAACTTATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
TTAAACTTAAACCAGATAAGTG
Found at i:65622043 original size:13 final size:14
Alignment explanation
Indices: 65622025--65622053 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
65622015 TAGATATTAT
65622025 TAAAATATTAA-TA
1 TAAAATATTAAGTA
65622038 TAAAATATTAAGTA
1 TAAAATATTAAGTA
65622052 TA
1 TA
65622054 TATTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAAAATATTAAGTA
Found at i:65622196 original size:13 final size:15
Alignment explanation
Indices: 65622161--65622191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65622151 TTTATGTTTA
65622161 ATAATATTGAAAATT
1 ATAATATTGAAAATT
*
65622176 ATAATATTTAAAATT
1 ATAATATTGAAAATT
65622191 A
1 A
65622192 ATATTGTATT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAATATTGAAAATT
Found at i:65622739 original size:2 final size:2
Alignment explanation
Indices: 65622732--65622773 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
65622722 TACGCCCTTT
65622732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65622774 GGAATATGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65622841 original size:18 final size:18
Alignment explanation
Indices: 65622818--65622853 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
65622808 TGAAAAATGG
65622818 TCGATTGGGTTTTAACTC
1 TCGATTGGGTTTTAACTC
65622836 TCGATTGGGTTTTAACTC
1 TCGATTGGGTTTTAACTC
65622854 GATTGGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGATTGGGTTTTAACTC
Found at i:65622856 original size:16 final size:17
Alignment explanation
Indices: 65622818--65622859 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
65622808 TGAAAAATGG
65622818 TCGATTGGGTTTTAACTC
1 TCGATTGGGTTTTAAC-C
65622836 TCGATTGGGTTTTAA-C
1 TCGATTGGGTTTTAACC
65622852 TCGATTGG
1 TCGATTGG
65622860 CATGAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.38
18 15 0.62
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (17 bp):
TCGATTGGGTTTTAACC
Found at i:65623632 original size:18 final size:18
Alignment explanation
Indices: 65623586--65623636 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
65623576 AGCTCTCAGG
65623586 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
65623604 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
65623622 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
65623637 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:65624356 original size:12 final size:12
Alignment explanation
Indices: 65624341--65624368 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65624331 GCCGTTTGTG
65624341 TGTTCGATATAA
1 TGTTCGATATAA
65624353 TGTTCGATATAA
1 TGTTCGATATAA
65624365 TGTT
1 TGTT
65624369 TTCTGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (12 bp):
TGTTCGATATAA
Found at i:65625793 original size:13 final size:13
Alignment explanation
Indices: 65625775--65625802 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
65625765 CTTCTACAAG
65625775 TAAACTTCATAAA
1 TAAACTTCATAAA
65625788 TAAACTTCATAAA
1 TAAACTTCATAAA
65625801 TA
1 TA
65625803 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTCATAAA
Found at i:65626260 original size:20 final size:20
Alignment explanation
Indices: 65626235--65626272 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
65626225 AATATTTTCC
*
65626235 AGTAAATCATTTTACAGACA
1 AGTAAAACATTTTACAGACA
*
65626255 AGTAAAACATTTTCCAGA
1 AGTAAAACATTTTACAGA
65626273 AATCATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (20 bp):
AGTAAAACATTTTACAGACA
Found at i:65626293 original size:14 final size:15
Alignment explanation
Indices: 65626255--65626297 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
65626245 TTTACAGACA
*
65626255 AGTAAAACATTTTCC
1 AGTAAAACATTTTAC
*
65626270 AG-AAATCATTTTAC
1 AGTAAAACATTTTAC
65626284 -GTAAAACATTTTAC
1 AGTAAAACATTTTAC
65626298 TGGCAATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 21 0.88
15 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (15 bp):
AGTAAAACATTTTAC
Found at i:65627878 original size:43 final size:44
Alignment explanation
Indices: 65627751--65627879 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
65627741 ATAGGATTTC
*
65627751 ATTATGTG-TTATCGTGTAAGACCGCGTCTGGGACGTTGGCATCG
1 ATTATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCG
* ** *
65627795 ACT-TGTGACTTACGTGTAAGACCTTGTCTGGGATAG-TGGCATCG
1 ATTATGTGA-TTACGTGTAAGACCACGTCTGGGA-CGTTGGCATCG
* *
65627839 -TTATGTGATTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 ATTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
65627880 TGTATGAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.01
43 31 0.44
44 34 0.49
45 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (44 bp):
ATTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
Found at i:65630303 original size:3 final size:3
Alignment explanation
Indices: 65630297--65630342 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
65630287 ATATGTTATT
65630297 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
65630343 ATGAAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:65631198 original size:16 final size:15
Alignment explanation
Indices: 65631177--65631206 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
65631167 GTGAGTTGGA
65631177 TATATATATGTATAAT
1 TATATATA-GTATAAT
65631193 TATATATAGTATAA
1 TATATATAGTATAA
65631207 ATGTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TATATATAGTATAAT
Found at i:65633205 original size:24 final size:24
Alignment explanation
Indices: 65633177--65633226 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
65633167 ATGAAGCTTG
65633177 AAATTATGTTAAACAACTTTTGCT
1 AAATTATGTTAAACAACTTTTGCT
65633201 AAATTATGTTAAACAACTTTTGCT
1 AAATTATGTTAAACAACTTTTGCT
65633225 AA
1 AA
65633227 GCGATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (24 bp):
AAATTATGTTAAACAACTTTTGCT
Found at i:65633236 original size:24 final size:24
Alignment explanation
Indices: 65633182--65633236 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
65633172 GCTTGAAATT
**
65633182 ATGTTAAACAACTTTTGCTAAATT
1 ATGTTAAACAACTTTTGCTAAACG
*
65633206 ATGTTAAACAACTTTTGCTAAGCG
1 ATGTTAAACAACTTTTGCTAAACG
*
65633230 ATTTTAA
1 ATGTTAA
65633237 GTGAAAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (24 bp):
ATGTTAAACAACTTTTGCTAAACG
Found at i:65633444 original size:30 final size:29
Alignment explanation
Indices: 65633376--65633447 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
65633366 TGAAGTTTAA
65633376 TTTCC-AAGCTTTGGGGAAAAAGTGTAATT
1 TTTCCAAAG-TTTGGGGAAAAAGTGTAATT
* * * * *
65633405 ATGCAAAAGTTTAGGGGCAAAATTGTAATT
1 TTTCCAAAGTTT-GGGGAAAAAGTGTAATT
65633435 TTTCCAAAGTTTG
1 TTTCCAAAGTTTG
65633448 AGTCAAGGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (29 bp):
TTTCCAAAGTTTGGGGAAAAAGTGTAATT
Found at i:65633893 original size:50 final size:50
Alignment explanation
Indices: 65633782--65634077 Score: 306
Period size: 50 Copynumber: 5.8 Consensus size: 50
65633772 ATTTGGGTAA
* * * *
65633782 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---CGA-GATG
* * *
65633837 AGAGGTCCCTTGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
65633887 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
65633937 AGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * ** * *
65633987 AAAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-ATACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** *
65634036 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
65634078 TGTTATTATC
Statistics
Matches: 210, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
49 39 0.19
50 129 0.61
51 2 0.01
54 1 0.00
55 39 0.19
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:65636404 original size:21 final size:21
Alignment explanation
Indices: 65636364--65636404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65636354 TCAAAGGTAA
*
65636364 ATAAACAATATCATACACTTT
1 ATAAACAATATCATAAACTTT
65636385 ATAAA-AATATCATCAAACTT
1 ATAAACAATATCAT-AAACTT
65636405 ACAACTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAACAATATCATAAACTTT
Found at i:65637136 original size:57 final size:58
Alignment explanation
Indices: 65637038--65637163 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 58
65637028 AAGGCATCGC
*
65637038 AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAAGAG
1 AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
* *** *
65637096 ATCACATCCCTTC-AAACACACTTGAGAGCACAC-AAGTGCTAAACCCGAAGGCAACAG
1 AACACATCCCTTCTAAACACACCAAAGAGCAC-CTAAGTGCTAAACCCAAAGGCAACAG
65637153 AACACATCCCT
1 AACACATCCCT
65637164 ATTGGCATGC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 47 0.78
58 13 0.22
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (58 bp):
AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
Done.