Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_pilon, whole genome shotgun sequence
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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 9 of 17
Found at i:1678141 original size:31 final size:29
Alignment explanation
Indices: 1678073--1678203 Score: 70
Period size: 31 Copynumber: 4.3 Consensus size: 29
1678063 ATATTATTTT
*
1678073 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1678103 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
1678136 TTATATTAATTATTTATTAAAGTAATAGT-G
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
1678166 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
1678194 GTATATTTTA
1 TTATATTTTA
1678204 AATATCTTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.12
28 12 0.16
30 8 0.11
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1678222 original size:23 final size:23
Alignment explanation
Indices: 1678173--1678223 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1678163 GTGTTATATT
**
1678173 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1678196 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1678219 ATATT
1 ATATT
1678224 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1678366 original size:34 final size:36
Alignment explanation
Indices: 1678328--1678412 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 36
1678318 TAAATTTTTT
1678328 TAATAATTTATTATATATTATTA-AA-A-TAAAAATA
1 TAAT-ATTTATTATATATTATTATAATATTAAAAATA
1678362 TAATATCTTA-TATTATATTATTATAATATTAAAAATA
1 TAATAT-TTATTA-TATATTATTATAATATTAAAAATA
1678399 TAATATTATATTAT
1 TAATATT-TATTAT
1678413 TAGAAATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
33 4 0.09
34 17 0.39
35 2 0.05
36 2 0.05
37 17 0.39
38 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
TAATATTTATTATATATTATTATAATATTAAAAATA
Found at i:1678405 original size:22 final size:22
Alignment explanation
Indices: 1678375--1678426 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1678365 TATCTTATAT
*
1678375 TATATTATTATAATATTAAAAA
1 TATAATATTATAATATTAAAAA
* *
1678397 TATAATATTATATTATTAGAAA
1 TATAATATTATAATATTAAAAA
1678419 TATTAATA
1 TA-TAATA
1678427 AATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAATATTATAATATTAAAAA
Found at i:1678406 original size:30 final size:32
Alignment explanation
Indices: 1678371--1678432 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
1678361 ATAATATCTT
*
1678371 ATATTATATTATTA-TAATATTAA-AAATATA
1 ATATTATATTATTAGAAATATTAATAAATATA
1678401 ATATTATATTATTAGAAATATTAATAAATATA
1 ATATTATATTATTAGAAATATTAATAAATATA
1678433 TTTTAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.48
31 8 0.28
32 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
ATATTATATTATTAGAAATATTAATAAATATA
Found at i:1678426 original size:37 final size:37
Alignment explanation
Indices: 1678346--1678427 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
1678336 TATTATATAT
** *
1678346 TATTAA-AATAAAAATATAATATCTTATATTATATTAT
1 TATTAATAATAAAAATATAATA-CTTATATTATAGAAA
*
1678383 TA-TAATATTAAAAATATAATA-TTATATTATTAGAAA
1 TATTAATAATAAAAATATAATACTTATATTA-TAGAAA
1678419 TATTAATAA
1 TATTAATAA
1678428 ATATATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
35 8 0.22
36 8 0.22
37 21 0.57
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
TATTAATAATAAAAATATAATACTTATATTATAGAAA
Found at i:1678431 original size:22 final size:22
Alignment explanation
Indices: 1678388--1678431 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1678378 ATTATTATAA
*
1678388 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1678410 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1678432 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1678713 original size:42 final size:42
Alignment explanation
Indices: 1678657--1678748 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1678647 TTCTTCCAAC
** * * *
1678657 CAAACACTTGAAAACATTTTCCGGAAAATGATTTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
1678699 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
1678741 CAAACACG
1 CAAACACG
1678749 AGATTTCGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
Found at i:1682087 original size:2 final size:2
Alignment explanation
Indices: 1682009--1682072 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
1681999 CGTTTGAGTT
1682009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
1682050 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1682073 TAGTTATTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1682157 original size:2 final size:2
Alignment explanation
Indices: 1682150--1682174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1682140 TGTGCATGTT
1682150 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 T
1682175 GGTTATATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1688852 original size:210 final size:211
Alignment explanation
Indices: 1688483--1688906 Score: 798
Period size: 211 Copynumber: 2.0 Consensus size: 211
1688473 AGATCCGCAT
1688483 CAGTGGATTACTATATATTTGCAACAATCCAAGTTGTATCCAACAACATTTTTGCGTGGTTTTAG
1 CAGTGGATTACTATATATTTGCAACAATCCAAGTTGTATCCAACAACATTTTTGCGTGGTTTTAG
1688548 GAGAATCCAACATTGATTATGACTCTCATTAAACGTTGGAGGTCGAAGATGCATACTTTCCATTT
66 GAGAATCCAACATTGATTATGACTCTCATTAAACGTTGGAGGTCGAAGATGCATACTTTCCATTT
1688613 TTCGAGTGGTGAAGCATCAATTAACATTGGAAGATGTCGCTT-ACCTGATGTTCCGGTTAACAGT
131 TTCGAGTGGTGAAGCATCAATTAACATTGGAAGATGTCGCTTAACCTGATGTTCCGGTTAACAGT
1688677 GCGACGATAGTTAGAC
196 GCGACGATAGTTAGAC
1688693 CAGTGGATTACTATATATTTGCAACAATCCAAGTTGTATCCAACAACATTTTTGCGTGGTTTTAA
1 CAGTGGATTACTATATATTTGCAACAATCCAAGTTGTATCCAACAACATTTTTGCGTGGTTTT-A
1688758 GGAGAATCCAACATTGATTATGACTCTCATTAAACGTTGGAGGTCGAAGATGCATACTTTCCATT
65 GGAGAATCCAACATTGATTATGACTCTCATTAAACGTTGGAGGTCGAAGATGCATACTTTCCATT
1688823 TTTCGAGTGGTGAAGCATCAATT-ACATTGGAAGATGTCGCTTACCAACCTGATGTTCCGGTTAA
130 TTTCGAGTGGTGAAGCATCAATTAACATTGGAAGATGTCGCTT---AACCTGATGTTCCGGTTAA
1688887 CAGTGCGACGATAGTTAGAC
192 CAGTGCGACGATAGTTAGAC
1688907 ACAACGATTT
Statistics
Matches: 209, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
210 82 0.39
211 89 0.43
214 38 0.18
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (211 bp):
CAGTGGATTACTATATATTTGCAACAATCCAAGTTGTATCCAACAACATTTTTGCGTGGTTTTAG
GAGAATCCAACATTGATTATGACTCTCATTAAACGTTGGAGGTCGAAGATGCATACTTTCCATTT
TTCGAGTGGTGAAGCATCAATTAACATTGGAAGATGTCGCTTAACCTGATGTTCCGGTTAACAGT
GCGACGATAGTTAGAC
Found at i:1690349 original size:28 final size:29
Alignment explanation
Indices: 1690298--1690352 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1690288 TCCCTAAAAT
* *
1690298 TTTCCAAATTTATACTTTGGCCACTAAAC
1 TTTCAAAATTTACACTTTGGCCACTAAAC
*
1690327 TTTCAAAATTTACA-TTTTGCCACTAA
1 TTTCAAAATTTACACTTTGGCCACTAA
1690353 CCAAAATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTCAAAATTTACACTTTGGCCACTAAAC
Found at i:1690789 original size:88 final size:89
Alignment explanation
Indices: 1690639--1690811 Score: 276
Period size: 88 Copynumber: 2.0 Consensus size: 89
1690629 AAAAAAGGAA
* * *
1690639 CAAAATAAAAAAGAATGGAGATGATAGAGCGTAAAGAAATGAGAGAAATTAAAGGTTGAGATTAA
1 CAAAATAAAAAAGAATGGAGATGATAGAGCATAAAGAAATGAGAAAAATTAAAGGCTGAGATTAA
*
1690704 CAATAGGAAACGAGAAGAACGCAT
66 CAATAGAAAACGAGAAGAACGCAT
*
1690728 CAAAAT-AAAAAGAATGGAGATGATAGATCATAAAGAAATGAGAAAAATTAAAGGCTGAGATTAA
1 CAAAATAAAAAAGAATGGAGATGATAGAGCATAAAGAAATGAGAAAAATTAAAGGCTGAGATTAA
* *
1690792 TAATAGAAAATGAGAAGAAC
66 CAATAGAAAACGAGAAGAAC
1690812 ATACTAAATC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 71 0.92
89 6 0.08
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.17
Consensus pattern (89 bp):
CAAAATAAAAAAGAATGGAGATGATAGAGCATAAAGAAATGAGAAAAATTAAAGGCTGAGATTAA
CAATAGAAAACGAGAAGAACGCAT
Found at i:1691050 original size:111 final size:116
Alignment explanation
Indices: 1690826--1691042 Score: 311
Period size: 111 Copynumber: 1.9 Consensus size: 116
1690816 TAAATCATGT
*
1690826 TTTTTGTCAATAATAAAAATATAATTAAAGAAATAAATAAAAGTAATATATGCAAATAATCAGTT
1 TTTTTGTCAATAATAAAAATATAATTAAAGAAATAAATAAAAGTAATATACGCAAATAATCAGTT
* *
1690891 CATCTAGTAGAATGAGATATTAGCTTCTTTAAGTAAGGTTAAGAATTCGTG
66 CATCTAGTAAAATGAGATATTAGATTCTTTAAGTAAGGTTAAGAATTCGTG
* *
1690942 TTTTTGTCAATAAT-AACA-AT-A-T-AAGAAATAAATAAAAGTAATTTACGCAAATAATCAGTT
1 TTTTTGTCAATAATAAAAATATAATTAAAGAAATAAATAAAAGTAATATACGCAAATAATCAGTT
* * *
1691002 CGTCTTGTAAAATGATG-TATTATATTCTTTAAGTAAGGTTA
66 CATCTAGTAAAATGA-GATATTAGATTCTTTAAGTAAGGTTA
1691043 GGGATTCGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
111 70 0.76
112 2 0.02
113 1 0.01
114 2 0.02
115 3 0.03
116 14 0.15
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (116 bp):
TTTTTGTCAATAATAAAAATATAATTAAAGAAATAAATAAAAGTAATATACGCAAATAATCAGTT
CATCTAGTAAAATGAGATATTAGATTCTTTAAGTAAGGTTAAGAATTCGTG
Found at i:1698143 original size:31 final size:32
Alignment explanation
Indices: 1698108--1698175 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
1698098 AATACTAAAA
*
1698108 TGAAATAAAAACTAAA-CTTTA-AGTATGCTTT
1 TGAAA-AAAAACTAAAGCTTTAGACTATGCTTT
* *
1698139 TG-AAAAAAATTAAAGGTTTAGACTATGCTTT
1 TGAAAAAAAACTAAAGCTTTAGACTATGCTTT
1698170 TGAAAA
1 TGAAAA
1698176 GAATTAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 9 0.29
30 6 0.19
31 13 0.42
32 3 0.10
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (32 bp):
TGAAAAAAAACTAAAGCTTTAGACTATGCTTT
Found at i:1699365 original size:20 final size:20
Alignment explanation
Indices: 1699340--1699536 Score: 164
Period size: 20 Copynumber: 9.7 Consensus size: 20
1699330 AATTGGGAAA
1699340 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
**
1699360 ATCGCAATGCGATTTTGTACT
1 ATCGCAATGCGATACTG-ACT
**
1699381 ATCGCAATGCGATTTTGTACT
1 ATCGCAATGCGATACTG-ACT
*
1699402 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1699422 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1699443 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1699463 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1699483 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * * *
1699503 TTCGCAACGTGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1699523 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1699537 TTTCTAAGCG
Statistics
Matches: 151, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.03
20 84 0.56
21 61 0.40
22 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1699385 original size:41 final size:40
Alignment explanation
Indices: 1699340--1699537 Score: 166
Period size: 41 Copynumber: 4.8 Consensus size: 40
1699330 AATTGGGAAA
* *
1699340 ATCGCAATGCGATACTGACTATCGCAATGCGATTTTGTACT
1 ATCGCAATGCGATAATGACTATCGCAATGCGATTCTG-ACT
** * *
1699381 ATCGCAATGCGATTTTGTACTATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATG-ACTATCGCAATGCGATTCTGACT
* * * *
1699422 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAATGCGATAATGAC--TATCGCAATGCGATTCTGACT
* * * * *
1699463 TTCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATGACTATCGCAATGCGATTCTGACT
* * *
1699503 TTCGCAACGTGATAAT-ACATAATCGCAATGCGATT
1 ATCGCAATGCGATAATGAC-T-ATCGCAATGCGATT
1699538 TTCTAAGCGC
Statistics
Matches: 129, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
39 4 0.03
40 32 0.25
41 74 0.57
42 19 0.15
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
ATCGCAATGCGATAATGACTATCGCAATGCGATTCTGACT
Found at i:1699732 original size:22 final size:22
Alignment explanation
Indices: 1699704--1699745 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1699694 CACTCTCTCA
1699704 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1699726 CCCATCTCCGGCGAAATCCG
1 CCCATCTCCGACGAAATCCG
1699746 GTCTATCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1700064 original size:20 final size:20
Alignment explanation
Indices: 1700010--1700068 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1700000 GCGATTCTCT
**
1700010 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1700030 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1700050 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1700069 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1700259 original size:25 final size:24
Alignment explanation
Indices: 1700205--1700259 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1700195 TGTTTATTAT
* *
1700205 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1700229 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1700255 TGTTT
1 TGTTT
1700260 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1701410 original size:18 final size:18
Alignment explanation
Indices: 1701389--1701433 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1701379 TCCACTTCGG
*
1701389 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1701407 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1701425 GAGCCATCA
1 GAGCCATCA
1701434 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1701940 original size:20 final size:20
Alignment explanation
Indices: 1701915--1701960 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1701905 TAGTTTACTT
1701915 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1701935 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1701955 TCGCAA
1 TCGCAA
1701961 TGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1701976 original size:19 final size:19
Alignment explanation
Indices: 1701954--1702021 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
1701944 GGAAATGGCT
1701954 ATCGCAATGAAAAATGAAA
1 ATCGCAATGAAAAATGAAA
* *
1701973 ATCGCAACG----A-CAAA
1 ATCGCAATGAAAAATGAAA
**
1701987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGAAAAATGAAA
1702006 ATCGCAATGACAAAAT
1 ATCGCAATGA-AAAAT
1702022 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
18 1 0.03
19 20 0.54
20 4 0.11
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.15
Consensus pattern (19 bp):
ATCGCAATGAAAAATGAAA
Found at i:1701989 original size:14 final size:14
Alignment explanation
Indices: 1701970--1702028 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1701960 ATGAAAAATG
1701970 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1701984 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
1702003 AAAATCGCAATGAC
1 AAAATCGCAACGAC
1702017 AAAATCGCAACG
1 AAAATCGCAACG
1702029 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1701991 original size:33 final size:33
Alignment explanation
Indices: 1701954--1702045 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
1701944 GGAAATGGCT
**
1701954 ATCGCAATGAAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1701987 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1702020 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1702046 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1702041 original size:19 final size:19
Alignment explanation
Indices: 1701984--1702050 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1701974 TCGCAACGAC
1701984 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
1702003 AAAATCGCAAT--G--A-C
1 AAAATCGCAATGCGAAATG
*
1702017 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
1702036 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
1702051 TTTGTGTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 25 0.64
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:1702081 original size:14 final size:14
Alignment explanation
Indices: 1702062--1702119 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1702052 TTGTGTTTCG
1702062 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1702076 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1702092 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1702108 CATTGCGATTTT
1 CGTTGCGATTTT
1702120 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1702100 original size:32 final size:33
Alignment explanation
Indices: 1702057--1702135 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1702047 GCGATTTGTG
* *
1702057 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1702089 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1702122 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1702136 AGCCATTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
Found at i:1702132 original size:19 final size:19
Alignment explanation
Indices: 1702078--1702177 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
1702068 GATTTTGTCG
1702078 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1702096 TTGCGA-TTT--TGT--CA
1 TTGCGATTTTCATTTCGCA
1702110 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
1702129 TTGCGATAGCCATTTCGCG
1 TTGCGATTTTCATTTCGCA
* **
1702148 TTGTGATAGTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
1702168 TTGCGATTTT
1 TTGCGATTTT
1702178 AAGTTTCGTG
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
14 8 0.12
15 3 0.05
16 2 0.03
17 2 0.03
18 9 0.14
19 27 0.42
20 13 0.20
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1704062 original size:14 final size:14
Alignment explanation
Indices: 1704043--1704078 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1704033 ATTGTTTAAT
1704043 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1704057 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1704071 TGATTTGT
1 TGATTTGT
1704079 TTAGTTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1704224 original size:14 final size:14
Alignment explanation
Indices: 1704205--1704258 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1704195 GAAACTGACT
*
1704205 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
1704219 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1704238 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1704252 ATCGCAA
1 ATCGCAA
1704259 TGCGATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1704242 original size:19 final size:17
Alignment explanation
Indices: 1704218--1704263 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
1704208 GCAACGAGAG
1704218 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
1704237 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
1704251 AATCGCAATGCGA
1 AATCGCAATGCGA
1704264 TTTTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:1704307 original size:20 final size:20
Alignment explanation
Indices: 1704282--1704359 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
1704272 TCGCATTGCA
*
1704282 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1704302 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1704322 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1704342 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1704360 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1704326 original size:40 final size:40
Alignment explanation
Indices: 1704282--1704359 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
1704272 TCGCATTGCA
1704282 ATTTTCTCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
1 ATTTTCTCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
1704322 ATTTTCTCGTTGCGATAGCCATTTTCGCGTTGCGATAG
1 ATTTTCTCGTTGCGATAGCCATTTTCGCGTTGCGATAG
1704360 TCAAATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (40 bp):
ATTTTCTCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
Found at i:1704725 original size:20 final size:20
Alignment explanation
Indices: 1704695--1704808 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
1704685 GATTCTGTAT
* *
1704695 TATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1704715 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1704735 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1704755 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1704776 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1704796 TATCGCATTGCGA
1 TATCGCGTTGCGA
1704809 TTTTCCCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1704811 original size:41 final size:41
Alignment explanation
Indices: 1704675--1704812 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
1704665 AACTTTGAAA
* * * *
1704675 ATCGCATTGCGATTCTGTATTATCTCGTTGCAAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** *
1704716 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
1704756 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1704797 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1704813 CCCAATTCGC
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 31 0.38
41 47 0.57
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1704823 original size:41 final size:41
Alignment explanation
Indices: 1704735--1704830 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
1704725 CGAAAGTCAG
* * ** *
1704735 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
1704776 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAA
1704818 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1704831 TTACTTATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 47 0.96
42 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:1707947 original size:64 final size:64
Alignment explanation
Indices: 1707879--1708035 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
1707869 TTGAAGGTGT
** *
1707879 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
1707941 GC
63 GC
* * * *
1707943 ATCGATGCATAAGGCA-TGCATCGATGTATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* *
1708007 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
1708036 ACCTTCATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:1708468 original size:28 final size:30
Alignment explanation
Indices: 1708412--1708468 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
1708402 TATGTGATAT
* *
1708412 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAACATGAAATGAGCTACATGAACACAA
1708442 GAGAA-ATGAAATGAG-TACATGAACACA
1 GAGAACATGAAATGAGCTACATGAACACA
1708469 TAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.44
29 9 0.36
30 5 0.20
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (30 bp):
GAGAACATGAAATGAGCTACATGAACACAA
Found at i:1708580 original size:15 final size:15
Alignment explanation
Indices: 1708548--1708581 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1708538 GAGGGTATAA
*
1708548 TAGTCCTTCGGGACG
1 TAGTCCTTCGAGACG
*
1708563 TAGTCCTTCGAGATG
1 TAGTCCTTCGAGACG
1708578 TAGT
1 TAGT
1708582 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGAGACG
Found at i:1710945 original size:3 final size:3
Alignment explanation
Indices: 1710937--1710966 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1710927 AAAGGGCCTA
*
1710937 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1710967 CTAATTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1717172 original size:27 final size:26
Alignment explanation
Indices: 1717120--1717174 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
1717110 AGTAAAAACA
*
1717120 GTGAAGGAGGAGATTTTAACAGAGAAT
1 GTGAAGGAGGAGATTTCAACA-AGAAT
1717147 GTGAGAGGAGGAGAGTTTCAAC-AGAAT
1 GTGA-AGGAGGAGA-TTTCAACAAGAAT
1717174 G
1 G
1717175 AGTGAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 10 0.40
28 9 0.36
29 6 0.24
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.20
Consensus pattern (26 bp):
GTGAAGGAGGAGATTTCAACAAGAAT
Found at i:1717181 original size:29 final size:27
Alignment explanation
Indices: 1717119--1717171 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1717109 CAGTAAAAAC
*
1717119 AGTGA-AGGAGGAGATTTTAACAGAGA
1 AGTGAGAGGAGGAGATTTCAACAGAGA
1717145 ATGTGAGAGGAGGAGAGTTTCAACAGA
1 A-GTGAGAGGAGGAGA-TTTCAACAGA
1717172 ATGAGTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 4 0.17
28 9 0.39
29 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.36, T:0.19
Consensus pattern (27 bp):
AGTGAGAGGAGGAGATTTCAACAGAGA
Found at i:1723039 original size:12 final size:12
Alignment explanation
Indices: 1723022--1723046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1723012 ACTGGTATCC
1723022 TTATATAGTATA
1 TTATATAGTATA
1723034 TTATATAGTATA
1 TTATATAGTATA
1723046 T
1 T
1723047 AGCATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATATAGTATA
Found at i:1726455 original size:2 final size:2
Alignment explanation
Indices: 1726448--1726477 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1726438 TTTATAGGTG
*
1726448 TA TA TA TA TA GA 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
1726478 AAACCATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1728602 original size:3 final size:3
Alignment explanation
Indices: 1728594--1728667 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
1728584 TTTTACTTAA
** * * * *
1728594 ATT ATT ATT -TT AAA ATT ACT ATT ATT ATT ATT ACTA AAT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
1728639 ATT ATT ATA ATT ATT A-T ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT
1728668 AAATAATTAC
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:1728642 original size:25 final size:24
Alignment explanation
Indices: 1728594--1728651 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1728584 TTTTACTTAA
*
1728594 ATTATTATT-TTAAAATTACTATT
1 ATTATTATTACTAAAATTACTATT
*
1728617 ATTATTATTACTAAATATTAGTATT
1 ATTATTATTACTAAA-ATTACTATT
*
1728642 ATTATAATTA
1 ATTATTATTA
1728652 TTATATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 9 0.30
24 4 0.13
25 17 0.57
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTATTATTACTAAAATTACTATT
Found at i:1730189 original size:4 final size:4
Alignment explanation
Indices: 1730180--1730204 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1730170 TATTTAGTCA
1730180 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1730205 TTCTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1731086 original size:29 final size:29
Alignment explanation
Indices: 1731007--1731094 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
1730997 TTAATTTATA
*
1731007 ATTATTTCTTTTAAAATTTTTTATA--TAT
1 ATTATTT-TTTTAATATTTTTTATATGTAT
* * * *
1731035 ACTTATTATTTTCATAATATTTATATGTAT
1 A-TTATTTTTTTAATATTTTTTATATGTAT
*
1731065 ATTATTTTTTTTATATTTTTTAT-TGT-T
1 ATTATTTTTTTAATATTTTTTATATGTAT
1731092 ATT
1 ATT
1731095 TTCAAGTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.08
28 17 0.35
29 23 0.48
30 4 0.08
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (29 bp):
ATTATTTTTTTAATATTTTTTATATGTAT
Found at i:1736086 original size:30 final size:30
Alignment explanation
Indices: 1736022--1736125 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
1736012 GTAAACACCA
*
1736022 TTTTTCAACACCAACACCTACCACCCCA-T
1 TTTTTCAACACCAACACCCACCACCCCATT
1736051 TTTTTCAACACCAACACCCACCACCCCATT
1 TTTTTCAACACCAACACCCACCACCCCATT
* *
1736081 TTTTTCAACACCAACACCCACCATCACATT
1 TTTTTCAACACCAACACCCACCACCCCATT
1736111 TTTTTCAACACCAAC
1 TTTTTCAACACCAAC
1736126 CTCATCATCC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 27 0.38
30 44 0.62
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (30 bp):
TTTTTCAACACCAACACCCACCACCCCATT
Found at i:1741657 original size:20 final size:22
Alignment explanation
Indices: 1741632--1741687 Score: 98
Period size: 20 Copynumber: 2.6 Consensus size: 22
1741622 TACATCTATA
1741632 CTCTTCAAAGATGATAGA-T-T
1 CTCTTCAAAGATGATAGATTCT
1741652 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
1741674 CTCTTCAAAGATGA
1 CTCTTCAAAGATGA
1741688 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 18 0.53
21 1 0.03
22 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:1742451 original size:36 final size:36
Alignment explanation
Indices: 1742393--1742526 Score: 133
Period size: 36 Copynumber: 3.7 Consensus size: 36
1742383 GATGTTCTCG
*
1742393 AAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTATCTCACTTGAGATTGTTTTTCTTA
* * ** ** **
1742430 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
*
1742466 AAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTATCTCACTTGAGATTGTTTTTCTTA
* * *
1742503 AAACAAGATTCATCTCGCTTGAGA
1 AAACAAAATTTATCTCACTTGAGA
1742527 CAGTTTCACT
Statistics
Matches: 74, Mismatches: 22, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
36 42 0.57
37 32 0.43
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
Found at i:1742489 original size:37 final size:36
Alignment explanation
Indices: 1742389--1742545 Score: 118
Period size: 36 Copynumber: 4.3 Consensus size: 36
1742379 GCCGGATGTT
** **
1742389 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTT
1 CTCGAAACA-AACTTTATCTCACTTGAGACAGTTTCA
** * * *
1742426 CTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 CTCGAAACAAACTTTATCTCACTTGAGACAGTTTCA
** **
1742462 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTT
1 CTCGAAACA-AACTTTATCTCACTTGAGACAGTTTCA
** * *
1742499 CTTAAAACAAGA-TTCATCTCGCTTGAGACAGTTTCA
1 CTCGAAACAA-ACTTTATCTCACTTGAGACAGTTTCA
*
1742535 CTAGAAACAAA
1 CTCGAAACAAA
1742546 AATTTCCATC
Statistics
Matches: 90, Mismatches: 28, Indels: 6
0.73 0.23 0.05
Matches are distributed among these distances:
35 1 0.01
36 54 0.60
37 35 0.39
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (36 bp):
CTCGAAACAAACTTTATCTCACTTGAGACAGTTTCA
Found at i:1742508 original size:73 final size:73
Alignment explanation
Indices: 1742389--1742543 Score: 274
Period size: 73 Copynumber: 2.1 Consensus size: 73
1742379 GCCGGATGTT
**
1742389 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
1 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCATCTCGCTTGAGA
1742454 CAGTTTCA
66 CAGTTTCA
*
1742462 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGA
1 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCATCTCGCTTGAGA
1742527 CAGTTTCA
66 CAGTTTCA
*
1742535 CTAGAAACA
1 CTCGAAACA
1742544 AAAATTTCCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.35
Consensus pattern (73 bp):
CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCATCTCGCTTGAGA
CAGTTTCA
Found at i:1742705 original size:3 final size:3
Alignment explanation
Indices: 1742697--1742779 Score: 71
Period size: 3 Copynumber: 27.7 Consensus size: 3
1742687 TTTTACTTAA
** * *
1742697 ATT ATT ATT -TT AAA ATT ATT ATT ATT ATT ATT ATT ACTA AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* * *
1742742 AGT ATT ATT ATA ATA ATT ATT ATT A-T ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT
1742780 AAATAATTAC
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.06
3 55 0.86
4 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1744328 original size:13 final size:13
Alignment explanation
Indices: 1744293--1744335 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1744283 TTAATTATTG
*
1744293 TTATTATTATTTAG
1 TTATT-TTATTTAT
*
1744307 TCATATTTATTTAT
1 TTAT-TTTATTTAT
1744321 TTATTTTATTTAT
1 TTATTTTATTTAT
1744334 TT
1 TT
1744336 TTCTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 13 0.52
15 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:1744342 original size:17 final size:17
Alignment explanation
Indices: 1744280--1744335 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1744270 GTTTTCAATA
*
1744280 TATTTAATTATTGTTA-T
1 TATTTATTTATT-TTATT
**
1744297 TA-TTATTTAGTCATATT
1 TATTTATTTA-TTTTATT
1744314 TATTTATTTATTTTATT
1 TATTTATTTATTTTATT
1744331 TATTT
1 TATTT
1744336 TTCTATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.26
17 16 0.52
18 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (17 bp):
TATTTATTTATTTTATT
Found at i:1745069 original size:3 final size:3
Alignment explanation
Indices: 1745053--1745108 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
1745043 TTTCATCTTT
* * * * * *
1745053 TTA TTA ATA ATA TTA TTG TTG TTA TTA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1745101 TTA TTA TT
1 TTA TTA TT
1745109 GTTAAATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1746619 original size:11 final size:11
Alignment explanation
Indices: 1746603--1746630 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1746593 ATTACTTTAA
1746603 TTATTATTTTC
1 TTATTATTTTC
1746614 TTATTATTTTC
1 TTATTATTTTC
1746625 TTATTA
1 TTATTA
1746631 GTCATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTC
Found at i:1747681 original size:19 final size:19
Alignment explanation
Indices: 1747657--1747693 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1747647 TATATCTTTG
1747657 TGAGAATTTATTCTCCGTT
1 TGAGAATTTATTCTCCGTT
1747676 TGAGAATTTATTCTCCGT
1 TGAGAATTTATTCTCCGT
1747694 GTCAGGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
TGAGAATTTATTCTCCGTT
Found at i:1748364 original size:36 final size:36
Alignment explanation
Indices: 1748313--1748384 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1748303 GAGATATGCA
* *
1748313 CACAAAGATCCTGTTATATTAATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
* *
1748349 CACAAAGATCTTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
1748385 TACGGCAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
Found at i:1749154 original size:35 final size:34
Alignment explanation
Indices: 1749099--1749168 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1749089 CATTCACATA
* *
1749099 TTTACATTTGCATTTGCATTTTTTATTTTTGCATT
1 TTTACATTTGCATTTACA-TTTTCATTTTTGCATT
* *
1749134 TTTACGTTTGTATTTACATTTTCATTTTTGCATT
1 TTTACATTTGCATTTACATTTTCATTTTTGCATT
1749168 T
1 T
1749169 GCATCTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTTCATTTTTGCATT
Found at i:1752295 original size:30 final size:30
Alignment explanation
Indices: 1752259--1752318 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1752249 CTCAAAGAAG
1752259 ACATATATGCTGGATCAACCTGACAGACCT
1 ACATATATGCTGGATCAACCTGACAGACCT
1752289 ACATATATGCTGGATCAACCTGACAGACCT
1 ACATATATGCTGGATCAACCTGACAGACCT
1752319 TACTTTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (30 bp):
ACATATATGCTGGATCAACCTGACAGACCT
Found at i:1753043 original size:17 final size:18
Alignment explanation
Indices: 1753021--1753054 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1753011 ATATTGGGTA
1753021 ACATTGGAACAG-ATTCT
1 ACATTGGAACAGCATTCT
1753038 ACATTGGAACAGCATTC
1 ACATTGGAACAGCATTC
1753055 CATAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (18 bp):
ACATTGGAACAGCATTCT
Found at i:1756165 original size:54 final size:54
Alignment explanation
Indices: 1756096--1756237 Score: 178
Period size: 54 Copynumber: 2.6 Consensus size: 54
1756086 AAATCACAGA
1756096 AAAGAATGAATGTGTTGTCAAATGCTTTACGAACATCTG-GCCAGAAGCCACAAG
1 AAAGAATGAATGTGTTGTCAAATGCTTTACGAACATCTGTG-CAGAAGCCACAAG
* * * * * *
1756150 AAAGGATGAATGTGTTATCAAACGCTTTACGAAAATCTGTGTAGAAGCCACGAG
1 AAAGAATGAATGTGTTGTCAAATGCTTTACGAACATCTGTGCAGAAGCCACAAG
* * * *
1756204 ATAGAATGAATGTATTGTCACATGTTTTACGAAC
1 AAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
1756238 CAGTGATTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (54 bp):
AAAGAATGAATGTGTTGTCAAATGCTTTACGAACATCTGTGCAGAAGCCACAAG
Found at i:1756629 original size:22 final size:22
Alignment explanation
Indices: 1756604--1756658 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1756594 ACATCTACAT
*
1756604 TCTTTAAAGATGATAGATTTTC
1 TCTTTAAAGATGATAGATTCTC
*
1756626 TCTTCAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
1756648 T-TTTCAAAGAT
1 TCTTT-AAAGAT
1756659 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:1756958 original size:4 final size:4
Alignment explanation
Indices: 1756949--1756979 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1756939 ATAGCATCAA
1756949 CATT CATT CATT CATT CATT CATT CATT CAT
1 CATT CATT CATT CATT CATT CATT CATT CAT
1756980 AAGAACGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:1757408 original size:45 final size:47
Alignment explanation
Indices: 1757344--1757434 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 47
1757334 CTATTTCCCA
* *
1757344 CATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
1757389 CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1757435 ATCTTTTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 29 0.71
46 4 0.10
47 8 0.20
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (47 bp):
CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
Found at i:1757505 original size:45 final size:45
Alignment explanation
Indices: 1757442--1757780 Score: 507
Period size: 45 Copynumber: 7.5 Consensus size: 45
1757432 GGGATCTTTT
*
1757442 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
1757487 TGATGTTTACAAAGCCTTCAGGTCATCTGTAAACCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1757532 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1757577 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCATTCAGTACA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1757622 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCATTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1757667 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
1757712 TGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1757757 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1757781 AGCTTTTTGA
Statistics
Matches: 268, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 256 0.96
46 4 0.01
47 8 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1757507 original size:25 final size:24
Alignment explanation
Indices: 1757476--1757552 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
1757466 ATCTGTAAGC
1757476 CCTTCAGTGCATGATGTTTACAAAG
1 CCTTCAGTGCATGATGTTT-CAAAG
* *
1757501 CCTTCAG-GTCAT-CTG--T-AAAC
1 CCTTCAGTG-CATGATGTTTCAAAG
1757521 CCTTCAGTGCATGATGTTTTCAAAG
1 CCTTCAGTGCATGATG-TTTCAAAG
1757546 CCTTCAG
1 CCTTCAG
1757553 GTCATCTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 13 0.32
21 3 0.07
22 1 0.02
24 4 0.10
25 20 0.49
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (24 bp):
CCTTCAGTGCATGATGTTTCAAAG
Found at i:1757799 original size:211 final size:209
Alignment explanation
Indices: 1757571--1758200 Score: 700
Period size: 211 Copynumber: 3.0 Consensus size: 209
1757561 TAAGCCTTTC
* * *
1757571 AGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCATTCAGTACATGATGTTTTCAAAA
1 AGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
* *
1757636 CCTTCGGGTCATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
66 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGC
1757701 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACAGTGTATGATGTTTT
131 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACAGTGTATGATGTTTT
1757766 CAAAAAGCCTTCGGG
196 -AAAAAGCCTTCGGG
*** * * *
1757781 AGCTTTTTGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 AG-TGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
* * * * **
1757846 ACCTTCGGGTCATATGTAAGCTCTTCAGTGCATGATGTTATCAAAACCTTCTGGTCATCCATAAG
65 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
* * * * * * * * ** * ***
1757911 ACCTACAGTGCAGGATATTTTCAAAAAGCCTTCGGGAGATTTTTTATGTTATCAAAACCT-TCG-
130 CCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGACA-TCTGTAAGTCCT-ACAGTGTAT-GA
* ** **
1757974 GGTCATATGTAAGCACTTC---
190 TGTTTTA-AAAAGC-CTTCGGG
* * *
1757993 AGTGCATGATGTTATCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAA
1 AGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1758058 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA-GATGTTTTCAAAACCTTCGGGTCATCTGTAAGC
66 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGC
* * * * *
1758122 CCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCCGTAAG-CCTTTCAGTGCATGATGATT
131 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCC-TACAGTGTATGATG-TT
*
1758186 TT-TAAAGCCTTCGGG
194 TTAAAAAGCCTTCGGG
1758201 TCATCTGTAA
Statistics
Matches: 330, Mismatches: 75, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
205 4 0.01
206 6 0.02
207 7 0.02
208 10 0.03
209 4 0.01
210 48 0.15
211 211 0.64
212 6 0.02
213 11 0.03
214 15 0.05
215 8 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (209 bp):
AGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACAGTGTATGATGTTTT
AAAAAGCCTTCGGG
Found at i:1757842 original size:45 final size:45
Alignment explanation
Indices: 1757788--1757946 Score: 183
Period size: 45 Copynumber: 3.5 Consensus size: 45
1757778 GGGAGCTTTT
* *
1757788 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1757833 TGATGTTTTCAAAACCTTCGGGTCATATGTAAGCTCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * ** * *
1757878 TGATGTTATCAAAACCTTCTGGTCATCCATAAGACCTACAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1757923 GGATATTTTCAAAAAGCCTTCGGG
1 TGATATTTTC-AAAA-CCTTCGGG
1757947 AGATTTTTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 84 0.88
46 4 0.04
47 7 0.07
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1757843 original size:76 final size:74
Alignment explanation
Indices: 1757712--1757854 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
1757702 CTTCAGTGCA
* * *
1757712 TGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACAGTGTATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGACATCTGTAAGCCCTACAGTGCATGATGTTTTC-AAAA-CCTT
1757777 CGGGAGCTTTT
64 CGGGAGCTTTT
* * *
1757788 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGACATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCG
1757853 GG
66 GG
1757855 TCATATGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 49 0.80
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGACATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:1757890 original size:121 final size:121
Alignment explanation
Indices: 1757667--1757891 Score: 371
Period size: 121 Copynumber: 1.9 Consensus size: 121
1757657 CTTCATTGCA
* *
1757667 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
1757732 GGACATCTGTAAGTCCTACAGTGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
66 GGACATATGTAAGTCCTACAGTGCATGATGTTATCAAAAAGCCTTCGGGAGCTTTT
1757788 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1757853 GGTCATATGTAAG-CTCTTCAGTGCATGATGTTATCAAAA
66 GGACATATGTAAGTC-CTACAGTGCATGATGTTATCAAAA
1757892 CCTTCTGGTC
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
120 1 0.01
121 95 0.99
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGACATATGTAAGTCCTACAGTGCATGATGTTATCAAAAAGCCTTCGGGAGCTTTT
Found at i:1757918 original size:166 final size:165
Alignment explanation
Indices: 1757622--1758230 Score: 736
Period size: 166 Copynumber: 3.6 Consensus size: 165
1757612 ATTCAGTACA
* *
1757622 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
1757687 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGACATCTGTAAGTCCTACA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGACCTACA
* *
1757752 GTGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
131 GTGCA-GATGTTTTCAAAAAGCCTTCGGGAGATTTT
* * *
1757788 TGATATTTTCAAAGCCTTCGGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * **
1757853 GGTCATATGTAAGCTCTTCAGTGCATGATGTTATCAAAACCTTCTGGTCATCCATAAGACCTACA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGACCTACA
*
1757918 GTGCAGGATATTTTCAAAAAGCCTTCGGGAGATTTT
131 GTGCA-GATGTTTTCAAAAAGCCTTCGGGAGATTTT
* * * * * *
1757954 TTATGTTATCAAAACCTTCGGGTCATATGTAAGCACTTCAGTGCATGATGTTATCAAAACCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1758019 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGACCTACA
*
1758084 GTGCAGATGTTTTC-AAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
131 GTGCAGATGTTTTCAAAAAGCCTTCGGG--A---G--A----TT---T--T
* * * * *
1758133 TGATGTTTTCAAAACCTTCAGGTCATCCGTAAGCCTTTCAGTGCATGATGATTTTTAAAGCCTTC
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAACCTTC
* * *
1758198 GGGTCATCTGTAAGACCTACAGTGCAGGATGTT
65 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTT
1758231 TTTAAATGAG
Statistics
Matches: 377, Mismatches: 49, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
163 8 0.02
164 4 0.01
165 9 0.02
166 268 0.71
168 1 0.00
170 1 0.00
174 2 0.01
177 1 0.00
179 43 0.11
180 40 0.11
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (165 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGACCTACA
GTGCAGATGTTTTCAAAAAGCCTTCGGGAGATTTT
Found at i:1758023 original size:45 final size:45
Alignment explanation
Indices: 1757956--1758230 Score: 408
Period size: 45 Copynumber: 6.1 Consensus size: 45
1757946 GAGATTTTTT
* *
1757956 ATGTTATCAAAACCTTCGGGTCATATGTAAGCACTTCAGTGCATG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1758001 ATGTTATCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1758046 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA-G
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1758090 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * * *
1758135 ATGTTTTCAAAACCTTCAGGTCATCCGTAAGCCTTTCAGTGCATG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * * * * *
1758180 ATGATTTTTAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGG
1 ATG-TTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1758226 ATGTT
1 ATGTT
1758231 TTTAAATGAG
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
44 43 0.20
45 132 0.62
46 37 0.17
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
Found at i:1758131 original size:89 final size:90
Alignment explanation
Indices: 1757956--1758230 Score: 417
Period size: 89 Copynumber: 3.1 Consensus size: 90
1757946 GAGATTTTTT
* * * *
1757956 ATGTTATCAAAACCTTCGGGTCATATGTAAGCACTTCAGTGCATGATGTTATCAAAACCTTCAGG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1758021 TCATCTGTAAGCCCTTCAGTGCATG
66 TCATCTGTAAGCCCTTCAGTGCATG
1758046 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA-GATGTTTTCAAAACCTTCGGG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1758110 TCATCTGTAAGCCCTTCAGTGCATG
66 TCATCTGTAAGCCCTTCAGTGCATG
* * * * * *
1758135 ATGTTTTCAAAACCTTCAGGTCATCCGTAAGCCTTTCAGTGCATGATGATTTTTAAAGCCTTCGG
1 ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAACCTTCGG
* * *
1758200 GTCATCTGTAAGACCTACAGTGCAGG
65 GTCATCTGTAAGCCCTTCAGTGCATG
1758226 ATGTT
1 ATGTT
1758231 TTTAAATGAG
Statistics
Matches: 170, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
89 83 0.49
90 45 0.26
91 42 0.25
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (90 bp):
ATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
TCATCTGTAAGCCCTTCAGTGCATG
Found at i:1758463 original size:3 final size:3
Alignment explanation
Indices: 1758448--1758510 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
1758438 TTTCATCTTT
* * * *
1758448 TTA TTA ATA TTA TTA TTG TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1758496 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1758511 AATAAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1760000 original size:12 final size:11
Alignment explanation
Indices: 1759966--1760018 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1759956 TTATTGTCTT
*
1759966 TTATTTTTTAA
1 TTATTATTTAA
1759977 -TA-TATTTAAA
1 TTATTATTT-AA
1759987 TTATTACTTTAA
1 TTATTA-TTTAA
*
1759999 TTATTATTTTA
1 TTATTATTTAA
1760010 TTATTATTT
1 TTATTATTT
1760019 TTGTATTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 15 0.42
12 10 0.28
13 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTATTTAA
Found at i:1760026 original size:11 final size:11
Alignment explanation
Indices: 1759951--1760019 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
1759941 TGCATTTTAT
*
1759951 TTTTATTATTG
1 TTTTATTATTA
*
1759962 TCTT-TTATT-
1 TTTTATTATTA
*
1759971 TTTTAATA-TA
1 TTTTATTATTA
*
1759981 TTTAAATTATTA
1 TTT-TATTATTA
*
1759993 CTTTAATTATTA
1 -TTTTATTATTA
1760005 TTTTATTATTA
1 TTTTATTATTA
1760016 TTTT
1 TTTT
1760020 TGTATTAGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 4 0.09
10 10 0.21
11 20 0.43
12 10 0.21
13 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:1760369 original size:18 final size:19
Alignment explanation
Indices: 1760346--1760401 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
1760336 TTTTTCCTTA
1760346 GAAATATCATATTG-AATT
1 GAAATATCATATTGAAATT
*
1760364 GAAATAACACTATTGTAAATT
1 GAAATATCA-TATTG-AAATT
*
1760385 -AAAT-TCATATTCAAATT
1 GAAATATCATATTGAAATT
1760402 CTTATATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.16
18 12 0.38
19 7 0.22
20 4 0.12
21 4 0.12
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (19 bp):
GAAATATCATATTGAAATT
Found at i:1760745 original size:25 final size:25
Alignment explanation
Indices: 1760711--1760759 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1760701 TCGTACCCGT
1760711 GCGAAAACCGATTACCACAATATGG
1 GCGAAAACCGATTACCACAATATGG
*
1760736 GCGAAAACCGGTTACCACAATATG
1 GCGAAAACCGATTACCACAATATG
1760760 TATGATGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
GCGAAAACCGATTACCACAATATGG
Found at i:1762449 original size:3 final size:3
Alignment explanation
Indices: 1762443--1762472 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1762433 CTTAAAAAAA
1762443 TAT TATT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
1762473 ATAAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1763452 original size:2 final size:2
Alignment explanation
Indices: 1763447--1763483 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1763437 GAGTTTGAAA
1763447 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1763484 GGTTTGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1774531 original size:16 final size:16
Alignment explanation
Indices: 1774487--1774540 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1774477 CATAAATTTT
1774487 TTTATATATTAACTTAAAA
1 TTTAT-TATTAACTT--AA
* *
1774506 ATTA-TATTAACTTAT
1 TTTATTATTAACTTAA
1774521 TTTATTATTAACTTAA
1 TTTATTATTAACTTAA
1774537 TTTA
1 TTTA
1774541 AAAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.13
16 14 0.47
17 9 0.30
19 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATTATTAACTTAA
Found at i:1774566 original size:27 final size:28
Alignment explanation
Indices: 1774518--1774572 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1774508 TATATTAACT
1774518 TATTTTATTATTAACTTAA-TTTAAAAA
1 TATTTTATTATTAACTTAATTTTAAAAA
* ** *
1774545 TATTTTATTTTTATTTTCATTTTAAAAA
1 TATTTTATTATTAACTTAATTTTAAAAA
1774573 ATGTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTATTATTAACTTAATTTTAAAAA
Found at i:1776208 original size:37 final size:37
Alignment explanation
Indices: 1776151--1776222 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 37
1776141 CCCCAATTTT
1776151 GCTTTGCCTTTTTTTGAATGCTTTTTGATTTTCAAAA
1 GCTTTGCCTTTTTTTGAATGCTTTTTGATTTTCAAAA
1776188 GCTTTGCCTTCTTTTT-AATGCTTTTTGATTTTCAA
1 GCTTTGCCTT-TTTTTGAATGCTTTTTGATTTTCAA
1776223 CTAAATTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 29 0.85
38 5 0.15
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (37 bp):
GCTTTGCCTTTTTTTGAATGCTTTTTGATTTTCAAAA
Found at i:1782008 original size:2 final size:2
Alignment explanation
Indices: 1782001--1782030 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1781991 ATTGAATCTG
1782001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1782031 GAGTTGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1802285 original size:64 final size:64
Alignment explanation
Indices: 1802232--1802394 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 64
1802222 CGGTGCACCA
*
1802232 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
1802296 CTTGTGCATCGATGCATCAAATGTATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * * *
1802361 AGAGTGCATCGGTGCATGGAGTGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1802395 CAATTAATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 38 0.46
65 44 0.54
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1802386 original size:17 final size:19
Alignment explanation
Indices: 1802342--1802381 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1802332 GAAAATATTC
1802342 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1802361 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1802380 AG
1 AG
1802382 TGCATTCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1802869 original size:21 final size:21
Alignment explanation
Indices: 1802827--1802869 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1802817 TTTCTGGGCT
* *
1802827 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1802848 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1802869 A
1 A
1802870 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1802942 original size:23 final size:22
Alignment explanation
Indices: 1802898--1802942 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1802888 AATCTCATAG
* *
1802898 GGGAACCGATTCTCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
1802920 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1802943 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1804457 original size:103 final size:103
Alignment explanation
Indices: 1804232--1804449 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1804222 GTCGAGGGTC
* *
1804232 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1804297 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1804335 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1804400 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1804438 TATGTGGTCCTT
1 TATGTGGTCCTT
1804450 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1804528 original size:23 final size:23
Alignment explanation
Indices: 1804465--1804533 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1804455 CATTATTTTA
*
1804465 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1804488 CGGCAC-TCTGATGCAATTCTACG
1 TGGCACTTC-GGTGCAATTCTACG
* *
1804511 TGGCACTTCGGTGTAATTATACG
1 TGGCACTTCGGTGCAATTCTACG
1804534 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 34 0.92
24 2 0.05
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1832090 original size:29 final size:29
Alignment explanation
Indices: 1832028--1832084 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1832018 CATTGGACTT
* *
1832028 TTTTAAAACTTGCATTTAGGTCCTCCAAC
1 TTTTAAAACTTACATATAGGTCCTCCAAC
1832057 TTTTAAAACTTACA-ATACGGTCCTCCAA
1 TTTTAAAACTTACATATA-GGTCCTCCAA
1832085 TATTTAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.35
Consensus pattern (29 bp):
TTTTAAAACTTACATATAGGTCCTCCAAC
Found at i:1844194 original size:14 final size:14
Alignment explanation
Indices: 1844177--1844213 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1844167 ACTGCTTACA
*
1844177 ACATAACACTTAAT
1 ACATAACACTGAAT
*
1844191 ACATAACACTGATT
1 ACATAACACTGAAT
1844205 ACATAACAC
1 ACATAACAC
1844214 ATGACCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (14 bp):
ACATAACACTGAAT
Found at i:1848018 original size:22 final size:22
Alignment explanation
Indices: 1847990--1848062 Score: 112
Period size: 22 Copynumber: 3.3 Consensus size: 22
1847980 CCTTCTTTTT
1847990 TCGCCGGCAGTCACAGCCTTCA
1 TCGCCGGCAGTCACAGCCTTCA
*
1848012 TCGCCGGCAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTTCA
*
1848034 TCGTCGGCAGTCACAG-CTTCCA
1 TCGCCGGCAGTCACAGCCTT-CA
1848056 TCGCCGG
1 TCGCCGG
1848063 GCGCTAACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 2 0.04
22 44 0.96
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (22 bp):
TCGCCGGCAGTCACAGCCTTCA
Found at i:1864016 original size:21 final size:21
Alignment explanation
Indices: 1863992--1864032 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1863982 ATTTTTGGCT
*
1863992 CAAAGGATCAATCCCTTTGAC
1 CAAAGGATCAATCCCCTTGAC
1864013 CAAAGGATCAATCCCCTTGA
1 CAAAGGATCAATCCCCTTGA
1864033 AAAATGATCG
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:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (21 bp):
CAAAGGATCAATCCCCTTGAC
Found at i:1865703 original size:24 final size:20
Alignment explanation
Indices: 1865676--1865733 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1865666 GCATGGGTAG
1865676 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
1865700 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
1865720 TGTATCGATGCACT
1 TGCATCGATGCACT
1865734 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1868324 original size:17 final size:16
Alignment explanation
Indices: 1868293--1868326 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1868283 CACGTGAGGA
1868293 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1868309 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1868326 T
1 T
1868327 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1873410 original size:20 final size:19
Alignment explanation
Indices: 1873387--1873426 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1873377 TCATTCATAT
* *
1873387 ATTATTTTATTTTTGTTTTA
1 ATTATTTAATTATT-TTTTA
1873407 ATTATTTAATTATTTTTTA
1 ATTATTTAATTATTTTTTA
1873426 A
1 A
1873427 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
ATTATTTAATTATTTTTTA
Found at i:1874285 original size:23 final size:23
Alignment explanation
Indices: 1874255--1874319 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
1874245 TACATATAGG
*
1874255 TCCCGAAGGACCACGTAGAATTA
1 TCCCGAAGGACCGCGTAGAATTA
*
1874278 TCCCGAAGTACCGCGTAGAATTA
1 TCCCGAAGGACCGCGTAGAATTA
1874301 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
1874320 CCCTCTACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.17
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTA
Found at i:1876126 original size:63 final size:62
Alignment explanation
Indices: 1876051--1876209 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
1876041 TTTGTTAAAG
* * * * *
1876051 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATAGAATGCCCTCA
** **
1876114 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATAGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATAGAATGCCCTCA
1876177 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
1876210 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATAGAATGCCCTCA
Found at i:1877599 original size:103 final size:103
Alignment explanation
Indices: 1877420--1877645 Score: 443
Period size: 103 Copynumber: 2.2 Consensus size: 103
1877410 GTCGATGGTC
*
1877420 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1877485 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1877523 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1877588 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1877626 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
1877646 TGTGGTCCTT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 122 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1877651 original size:18 final size:18
Alignment explanation
Indices: 1877628--1877663 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1877618 AGGAATGATA
1877628 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1877646 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1877664 ATATGTATTC
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:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1877739 original size:121 final size:121
Alignment explanation
Indices: 1877525--1877888 Score: 665
Period size: 121 Copynumber: 3.0 Consensus size: 121
1877515 AGGAATGATA
1877525 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1877590 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1877646 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1877711 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* * *
1877767 TGTGGTCCTTTGTGACATATATGTATTCTTTGGAACATGTGTGAAGCCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
1877832 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1877888 T
1 T
1877889 ATTATATGGC
Statistics
Matches: 235, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 235 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:1877786 original size:62 final size:62
Alignment explanation
Indices: 1877599--1877786 Score: 135
Period size: 62 Copynumber: 3.1 Consensus size: 62
1877589 TGATCCCTAG
* * *
1877599 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACATTGTGGTCCTTTGAGA
* * * * * * * *
1877661 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGTCTGGT-GAGACACATACT-TGATCC-CT
1 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCT-TTCG-G-GACAT--TGTGGTCCTTT
1877718 -AG-
59 GAGA
*
1877720 CATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACATTGTGGTCCTTTGTGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACATTGTGGTCCTTTGAGA
1877782 CATAT
1 CATAT
1877787 ATGTATTCTT
Statistics
Matches: 89, Mismatches: 20, Indels: 34
0.62 0.14 0.24
Matches are distributed among these distances:
57 6 0.07
58 5 0.06
59 19 0.21
60 12 0.13
61 11 0.12
62 25 0.28
63 5 0.06
64 6 0.07
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACATTGTGGTCCTTTGAGA
Found at i:1877963 original size:23 final size:23
Alignment explanation
Indices: 1877895--1877955 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1877885 CATTATTATA
*
1877895 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
1877918 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
1877941 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
1877956 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:1881778 original size:19 final size:20
Alignment explanation
Indices: 1881749--1881786 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1881739 AGAAATTTGT
1881749 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
1881769 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
1881787 GCAATGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:1883179 original size:18 final size:18
Alignment explanation
Indices: 1883156--1883191 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1883146 AGGAATGATA
*
1883156 TGTGGTCTTTCAGGACAT
1 TGTGGTCCTTCAGGACAT
*
1883174 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
1883192 ATATGTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:1883300 original size:18 final size:18
Alignment explanation
Indices: 1883277--1883312 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1883267 AGGAATGATA
1883277 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
1883295 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
1883313 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1883340 original size:121 final size:121
Alignment explanation
Indices: 1883057--1883416 Score: 631
Period size: 121 Copynumber: 3.0 Consensus size: 121
1883047 CGAGGGTCTA
1883057 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1883122 GATCCCTAGC-TATG--TAT-ATTCTTAAGGAATGATATGTGGTCTTTCAGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
1883174 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1883239 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
* *
1883295 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1883360 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT-ATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCA-GGACAT
1883416 T
1 T
1883417 ATTATATGGC
Statistics
Matches: 232, Mismatches: 6, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
117 75 0.32
118 4 0.02
120 3 0.01
121 150 0.65
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
Found at i:1883491 original size:23 final size:23
Alignment explanation
Indices: 1883423--1883483 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1883413 CATTATTATA
1883423 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
1883446 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
1883469 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
1883484 TTTATATGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:1888235 original size:22 final size:21
Alignment explanation
Indices: 1888210--1888253 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1888200 AATGTTGGAG
*
1888210 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
1888232 GGGAACTGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
1888253 G
1 G
1888254 TATTGTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:1890560 original size:17 final size:17
Alignment explanation
Indices: 1890531--1890564 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1890521 TCTCTTGCTC
1890531 ATGATGGAAAAGAAGAA
1 ATGATGGAAAAGAAGAA
1890548 ATGA-GGAAGAAGAAGAA
1 ATGATGGAA-AAGAAGAA
1890565 GATAACTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (17 bp):
ATGATGGAAAAGAAGAA
Found at i:1890754 original size:47 final size:46
Alignment explanation
Indices: 1890666--1890803 Score: 133
Period size: 47 Copynumber: 3.0 Consensus size: 46
1890656 ACACCCCTAA
* * *
1890666 TTTTTTCAATCTCATTTTTTA-CTTATATAATTTAGGCCCCTAATTTT
1 TTTTTTCAATCTCACTTTTTACCTT-TATAA-TTATGTCCCTAATTTT
* *
1890713 TTTTTTCAATCTCACATTTTACCTTTAAAATTGATGTCCCT-A--TT
1 TTTTTTCAATCTCACTTTTTACCTTTATAATT-ATGTCCCTAATTTT
* * * *
1890757 TTTTTT-AATATGACTTTTTACCTTTATAATTATATTCCTAATTTT
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTATGTCCCTAATTTT
1890802 TT
1 TT
1890804 CAATCATACT
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
42 6 0.08
43 22 0.29
44 8 0.11
45 4 0.05
46 3 0.04
47 29 0.39
48 3 0.04
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.56
Consensus pattern (46 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATTATGTCCCTAATTTT
Found at i:1890776 original size:43 final size:41
Alignment explanation
Indices: 1890711--1890824 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
1890701 GCCCCTAATT
* * *
1890711 TTTTTTTTCAATCTCACATTTTACCTTTAAAATTGATGTCCCTA
1 TTTTTTTT-AATAT-ACTTTTTACCTTTAAAATT-ATATCCCTA
* *
1890755 TTTTTTTTAATATGACTTTTTACCTTTATAATTATATTCCTA
1 TTTTTTTTAATAT-ACTTTTTACCTTTAAAATTATATCCCTA
* * *
1890797 ATTTTTTCAATCATACTTTTTACTTTTA
1 TTTTTTTTAAT-ATACTTTTTACCTTTA
1890825 TAGTTTAAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 29 0.48
43 23 0.38
44 8 0.13
ACGTcount: A:0.25, C:0.16, G:0.03, T:0.56
Consensus pattern (41 bp):
TTTTTTTTAATATACTTTTTACCTTTAAAATTATATCCCTA
Found at i:1890840 original size:43 final size:43
Alignment explanation
Indices: 1890659--1890843 Score: 144
Period size: 43 Copynumber: 4.2 Consensus size: 43
1890649 GGATGTTACA
* *
1890659 CCCCTAATTTTTTCAATCTCATTTTTTA-CTTATATAATTTAGG
1 CCCCTAATTTTTTCAATCTCACTTTTTACCTT-TATAATTTAAG
* * * *
1890702 CCCCTAATTTTTTTTTTCAATCTCACATTTTACCTTTAAAATTGATG
1 CCCCTAA----TTTTTTCAATCTCACTTTTTACCTTTATAATTTAAG
* * * * *
1890749 TCCCTATTTTTTTTAATATGACTTTTTACCTTTATAA-TTATA-
1 CCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTTA-AG
** * *
1890791 TTCCTAATTTTTTCAATCAT-ACTTTTTACTTTTATAGTTTAAG
1 CCCCTAATTTTTTCAATC-TCACTTTTTACCTTTATAATTTAAG
1890834 CCCCTAATTT
1 CCCCTAATTT
1890844 AATCATTTTT
Statistics
Matches: 111, Mismatches: 22, Indels: 18
0.74 0.15 0.12
Matches are distributed among these distances:
42 32 0.29
43 44 0.40
47 32 0.29
48 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.52
Consensus pattern (43 bp):
CCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTTAAG
Found at i:1891601 original size:93 final size:93
Alignment explanation
Indices: 1891442--1891621 Score: 351
Period size: 93 Copynumber: 1.9 Consensus size: 93
1891432 AAGTTGGGAC
*
1891442 AAGGGACTCAAGGTGAAGGAGTTTTTTCTGACTCAACAAGGACAACTGAAAAAGTTGGACACCTT
1 AAGGGACTCAAGGTGAAGGAGATTTTTCTGACTCAACAAGGACAACTGAAAAAGTTGGACACCTT
1891507 GAAGGCAACATTTCACCATCTTTATATT
66 GAAGGCAACATTTCACCATCTTTATATT
1891535 AAGGGACTCAAGGTGAAGGAGATTTTTCTGACTCAACAAGGACAACTGAAAAAGTTGGACACCTT
1 AAGGGACTCAAGGTGAAGGAGATTTTTCTGACTCAACAAGGACAACTGAAAAAGTTGGACACCTT
1891600 GAAGGCAACATTTCACCATCTT
66 GAAGGCAACATTTCACCATCTT
1891622 CAGATATATT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (93 bp):
AAGGGACTCAAGGTGAAGGAGATTTTTCTGACTCAACAAGGACAACTGAAAAAGTTGGACACCTT
GAAGGCAACATTTCACCATCTTTATATT
Found at i:1906320 original size:126 final size:125
Alignment explanation
Indices: 1906166--1906421 Score: 503
Period size: 125 Copynumber: 2.0 Consensus size: 125
1906156 GTTCGGTCTG
1906166 TAAATGACATTAATTTCATCCATTAAGTGACACGTTTCACAATATGGTAATTTTGAAATTTATTT
1 TAAATGACATTAATTTCATCCATTAAGTGACACGTTTCACAATATGGTAATTTTGAAATTTA-TT
1906231 TTAAAGAAAATATTAAAAATATTATTATATTTATAAAAAAACCCTAATTTCTCTTAAATTA
65 TTAAAGAAAATATTAAAAATATTATTATATTTATAAAAAAACCCTAATTTCTCTTAAATTA
1906292 TAAATGACATTAATTTCATCCATTAAGTGACACGTTTCACAATATGGTAATTTTGAAATTTATTT
1 TAAATGACATTAATTTCATCCATTAAGTGACACGTTTCACAATATGGTAATTTTGAAATTTATTT
1906357 TAAAGAAAATATTAAAAATATTATTATATTTATAAAAAAACCCTAATTTCTCTTAAATTA
66 TAAAGAAAATATTAAAAATATTATTATATTTATAAAAAAACCCTAATTTCTCTTAAATTA
1906417 TAAAT
1 TAAAT
1906422 AAACTCAAAA
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 68 0.52
126 62 0.48
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.40
Consensus pattern (125 bp):
TAAATGACATTAATTTCATCCATTAAGTGACACGTTTCACAATATGGTAATTTTGAAATTTATTT
TAAAGAAAATATTAAAAATATTATTATATTTATAAAAAAACCCTAATTTCTCTTAAATTA
Done.