Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 55
Found at i:3472812 original size:34 final size:35
Alignment explanation
Indices: 3472738--3472830 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 35
3472728 ATAATATAGT
*
3472738 TTTTGAAAATATATATTATATAGTTTTGAAAATGAT
1 TTTTGAAAATATATATTATATAGTTTTGAAAA-GAC
*
3472774 TTTTGAAAATATATATTATATAGTTTTGAAAA-CC
1 TTTTGAAAATATATATTATATAGTTTTGAAAAGAC
*
3472808 TTTTGAATATATATATATATATA
1 TTTTGAAAATATATAT-TATATA
3472831 TATATATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 15 0.28
35 6 0.11
36 32 0.60
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (35 bp):
TTTTGAAAATATATATTATATAGTTTTGAAAAGAC
Found at i:3472821 original size:2 final size:2
Alignment explanation
Indices: 3472814--3472881 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
3472804 AACCTTTTGA
3472814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3472856 AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3472882 GTTTTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3472908 original size:38 final size:39
Alignment explanation
Indices: 3472864--3472994 Score: 155
Period size: 38 Copynumber: 3.4 Consensus size: 39
3472854 ATATATATAT
3472864 ATATATATATATAATATAGTTTTTGAAAACA-TTTGAAAAC
1 ATATATATA-AT-ATATAGTTTTTGAAAACATTTTGAAAAC
3472904 ATATATATAATATATAGTTTTTGAAAACATTTTG-AAA-
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
* * * *
3472941 ATAAATATAATATAT-GGTATTAAAAACATTTTGTAAAA-
1 ATATATATAATATATAGTTTTTGAAAACATTTTG-AAAAC
*
3472979 ATAAATATAATATATA
1 ATATATATAATATATA
3472995 TATATATATA
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
36 15 0.18
37 14 0.17
38 39 0.47
39 6 0.07
40 9 0.11
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (39 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:3473030 original size:12 final size:12
Alignment explanation
Indices: 3473015--3473090 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
3473005 TATTAAATAA
3473015 TATTATTTTTAT
1 TATTATTTTTAT
*
3473027 TATTATTTATAT
1 TATTATTTTTAT
3473039 TATTTATTATTTAT
1 TA-TTATT-TTTAT
*
3473053 TA-TATTATTACT
1 TATTATTTTTA-T
*
3473065 TATT-TATTTAAT
1 TATTAT-TTTTAT
3473077 T-TTATTTTT-T
1 TATTATTTTTAT
3473087 TATT
1 TATT
3473091 TCAGGTCCAG
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.04
11 10 0.20
12 24 0.47
13 9 0.18
14 6 0.12
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTATTTTTAT
Found at i:3473044 original size:19 final size:19
Alignment explanation
Indices: 3473018--3473091 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
3473008 TAAATAATAT
3473018 TATT-TTTATTATTATTTA
1 TATTATTTATTATTATTTA
3473036 TATTATTTATTATT-TATTA
1 TATTATTTATTATTAT-TTA
3473055 TATTA-TTACTTATTTATTTAA
1 TATTATTTA-TTA-TTATTT-A
*
3473076 TTTTATTT-TT-TTATTT
1 TATTATTTATTATTATTT
3473092 CAGGTCCAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
18 14 0.29
19 20 0.42
20 6 0.12
21 6 0.12
22 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTATTTATTATTATTTA
Found at i:3473078 original size:5 final size:4
Alignment explanation
Indices: 3473029--3473091 Score: 51
Period size: 4 Copynumber: 15.5 Consensus size: 4
3473019 ATTTTTATTA
*
3473029 TTAT TTAT ATTAT TTA- TTAT TTA- TTAT ATTA- TTAC TTAT TTAT TTAATT
1 TTAT TTAT -TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TT-A-T
*
3473078 TTAT TTTT TTAT TT
1 TTAT TTAT TTAT TT
3473092 CAGGTCCAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
3 9 0.18
4 28 0.57
5 9 0.18
6 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:3475334 original size:31 final size:30
Alignment explanation
Indices: 3475288--3475367 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
3475278 CGATAATATA
*
3475288 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
3475319 TATTAATAATTTTATAATCCTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
3475350 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
3475368 TTTTTAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:3476131 original size:31 final size:30
Alignment explanation
Indices: 3476096--3476182 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
3476086 TCAATAAAGT
3476096 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
** *
3476127 TTAAAGGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
3476158 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
3476183 TATTATCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:3476505 original size:20 final size:20
Alignment explanation
Indices: 3476480--3476585 Score: 149
Period size: 20 Copynumber: 5.3 Consensus size: 20
3476470 AATTTGTAAA
*
3476480 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
3476500 TTGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
3476520 TCGCAACATAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
3476540 TCGCAATACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
3476560 TCACAACACAGAAGTCAAAC
1 TCGCAACACAAAAGTCAAAT
3476580 TCGCAA
1 TCGCAA
3476586 AGCGCATTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:3476604 original size:19 final size:20
Alignment explanation
Indices: 3476580--3476641 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
3476570 GAAGTCAAAC
*
3476580 TCGCAAAGCGCA-TTTATTT
1 TCGCAAAGCGAATTTTATTT
* *
3476599 TCGCAACGTGAATTTTATTT
1 TCGCAAAGCGAATTTTATTT
*
3476619 TCGCAATGCGAATTTTATTT
1 TCGCAAAGCGAATTTTATTT
3476639 TCG
1 TCG
3476642 AATTCAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 9 0.24
20 28 0.76
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (20 bp):
TCGCAAAGCGAATTTTATTT
Found at i:3476617 original size:20 final size:20
Alignment explanation
Indices: 3476592--3476641 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3476582 GCAAAGCGCA
*
3476592 TTTATTTTCGCAACGTGAAT
1 TTTATTTTCGCAACGCGAAT
*
3476612 TTTATTTTCGCAATGCGAAT
1 TTTATTTTCGCAACGCGAAT
3476632 TTTATTTTCG
1 TTTATTTTCG
3476642 AATTCAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTATTTTCGCAACGCGAAT
Found at i:3476776 original size:22 final size:22
Alignment explanation
Indices: 3476751--3476805 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3476741 CTCCTCTCTA
*
3476751 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
3476773 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
3476795 CGGCGAAATCC
1 CGACGAAATCC
3476806 ATCTATCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.45, G:0.16, T:0.16
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:3477176 original size:20 final size:20
Alignment explanation
Indices: 3477129--3477179 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3477119 AAACTTAAAT
*
3477129 TCGCAACACGAAAATAAAAA
1 TCGCAACGCGAAAATAAAAA
* * *
3477149 TCACAACGCGAACATGAAAA
1 TCGCAACGCGAAAATAAAAA
3477169 TCGCAACGCGA
1 TCGCAACGCGA
3477180 TTTTAGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAAATAAAAA
Found at i:3477209 original size:20 final size:20
Alignment explanation
Indices: 3477176--3477259 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
3477166 AAATCGCAAC
*
3477176 GCGATTTT-AGTTTCACGTT
1 GCGATTTTCATTTTCACGTT
* *
3477195 GCGATTTTTATTTTCGCGTT
1 GCGATTTTCATTTTCACGTT
* *
3477215 ACGATTTTCATGTTCACGTT
1 GCGATTTTCATTTTCACGTT
*
3477235 GCGATTTTCATTTTTCGCGTT
1 GCGATTTTCA-TTTTCACGTT
3477256 GCGA
1 GCGA
3477260 ATTTAAGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.15
20 34 0.63
21 12 0.22
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCACGTT
Found at i:3479255 original size:19 final size:19
Alignment explanation
Indices: 3479231--3479267 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3479221 TTTCGGCATT
* *
3479231 ATTTATTTATTTATTTATG
1 ATTTATGTATTAATTTATG
3479250 ATTTATGTATTAATTTAT
1 ATTTATGTATTAATTTAT
3479268 TTTCAGCGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTATGTATTAATTTATG
Found at i:3479512 original size:21 final size:21
Alignment explanation
Indices: 3479413--3479529 Score: 117
Period size: 21 Copynumber: 5.6 Consensus size: 21
3479403 ATGCACCTAT
* *
3479413 CATCGTTCAAAAGGCGCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
3479434 TATCGTTCAAGATGCGCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
3479455 TATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
* *
3479476 CATCATTGAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
3479497 CACCGTTCAAGAGGCCTCTGT
1 CATCGTTCAAGAGGCCCCTCC
3479518 CATCGTTCAAGA
1 CATCGTTCAAGA
3479530 AGTCCCACCC
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:3479545 original size:42 final size:42
Alignment explanation
Indices: 3479458--3479551 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
3479448 CGCCTCCTAT
* * *
3479458 CGTTCAAGAGGCCCCTCTCATCATTGAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGCCCCACCCAC
* * * * *
3479500 CGTTCAAGAGGCCTCTGTCATCGTTCAAGAAGTCCCACCCGC
1 CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGCCCCACCCAC
3479542 CGTTCAAGAG
1 CGTTCAAGAG
3479552 CCAGATTCAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCATTCAAGAAGCCCCACCCAC
Found at i:3481171 original size:40 final size:40
Alignment explanation
Indices: 3481111--3481240 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
3481101 AACACGAAAA
* * *
3481111 TCAAATTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAG
1 TCAAATTCGCAACACAAAAGTCAAATTCGCATTGCGATAG
*
3481151 TCAAATTCACAACACAAAAGTCAAATTCGCATTGCGATAG
1 TCAAATTCGCAACACAAAAGTCAAATTCGCATTGCGATAG
** * ** *
3481191 TCAAATTCGCAACATTAAAGTTAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACACAAAAGTCAAATTCGCATTGCGATAG
3481231 TCAAATTCGC
1 TCAAATTCGC
3481241 GTTGCGATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (40 bp):
TCAAATTCGCAACACAAAAGTCAAATTCGCATTGCGATAG
Found at i:3481247 original size:20 final size:20
Alignment explanation
Indices: 3481105--3481240 Score: 137
Period size: 20 Copynumber: 6.8 Consensus size: 20
3481095 GTTGAAAACA
*
3481105 CGAAAATCAAATTCGCAACG
1 CGAAAGTCAAATTCGCAACG
***
3481125 CGAAAGTCAAATTCGCGTTG
1 CGAAAGTCAAATTCGCAACG
* * *
3481145 CGATAGTCAAATTCACAACA
1 CGAAAGTCAAATTCGCAACG
* **
3481165 CAAAAGTCAAATTCGCATTG
1 CGAAAGTCAAATTCGCAACG
* *
3481185 CGATAGTCAAATTCGCAACA
1 CGAAAGTCAAATTCGCAACG
** *
3481205 TTAAAGTTAAATTCGCAACG
1 CGAAAGTCAAATTCGCAACG
3481225 CGAAAGTCAAATTCGC
1 CGAAAGTCAAATTCGC
3481241 GTTGCGATTT
Statistics
Matches: 87, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAACG
Found at i:3481556 original size:18 final size:18
Alignment explanation
Indices: 3481530--3481570 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3481520 AGGTGAAGCC
* *
3481530 GATTGTGATTGGGATTTT
1 GATTTTGATTGCGATTTT
3481548 GATTTTGATTGCGATTTT
1 GATTTTGATTGCGATTTT
3481566 GATTT
1 GATTT
3481571 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:3484842 original size:19 final size:19
Alignment explanation
Indices: 3484801--3484949 Score: 244
Period size: 19 Copynumber: 7.7 Consensus size: 19
3484791 GTAAATTCGT
* *
3484801 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
*
3484821 GTTACGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484840 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484859 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484878 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484897 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484916 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
3484935 GTGTTGCGAATTTGA
1 --GTTGCGAATTTGA
3484950 CTTCTGTGTT
Statistics
Matches: 123, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
19 95 0.77
20 15 0.12
21 13 0.11
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:3484960 original size:20 final size:20
Alignment explanation
Indices: 3484916--3485043 Score: 211
Period size: 20 Copynumber: 6.3 Consensus size: 20
3484906 TTGAAATTCA
* *
3484916 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
3484937 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
3484957 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
3484977 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
3484997 GTTGCGAATTTGAATTCTGT
1 GTTGCGAATTTGACTTCTGT
3485017 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
3485037 GTTGCGA
1 GTTGCGA
3485044 TTTACAAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
20 89 0.88
21 12 0.12
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:3484979 original size:40 final size:40
Alignment explanation
Indices: 3484840--3485043 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
3484830 TTGAAATTCA
* * *
3484840 GTTGCGAATTTGAAATTC--AGTTGCGAATTTGAAATTC--A
1 GTTGCGAATTTG-AATTCTGTGTTGCGAATTTG-ACTTCTGT
* * *
3484878 GTTGCGAATTTGAAATTC--AGTTGCGAATTTGAAATTC--A
1 GTTGCGAATTTG-AATTCTGTGTTGCGAATTTG-ACTTCTGT
*
3484916 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTG-AATTCTGTGTTGCGAATTTGACTTCTGT
* *
3484957 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCTGT
3484997 GTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCTGT
3485037 GTTGCGA
1 GTTGCGA
3485044 TTTACAAATT
Statistics
Matches: 154, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
38 56 0.36
39 4 0.03
40 82 0.53
41 12 0.08
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCTGT
Found at i:3484999 original size:60 final size:61
Alignment explanation
Indices: 3484799--3485043 Score: 244
Period size: 60 Copynumber: 4.1 Consensus size: 61
3484789 AAGTAAATTC
* * * * * *
3484799 GTGTTGCGAATTCGAAAATC-GAGTTACGAATTTGAAATTC--AGTTGCGAATTTGAAATTC-
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTG-AATTCTGTGTTGCGAATTTG-ACTTCT
* * *
3484858 -AGTTGCGAATTTGAAATTCA--GTTGCGAATTTGAAATTC--AGTTGCGAATTTGAAATTC-
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTG-AATTCTGTGTTGCGAATTTG-ACTTCT
* * *
3484915 -AGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCT
* *
3484975 GTGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCT
3485035 GTGTTGCGA
1 GTGTTGCGA
3485044 TTTACAAATT
Statistics
Matches: 166, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
57 56 0.34
58 20 0.12
59 15 0.09
60 63 0.38
61 12 0.07
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.40
Consensus pattern (61 bp):
GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAATTCTGTGTTGCGAATTTGACTTCT
Found at i:3485060 original size:20 final size:20
Alignment explanation
Indices: 3485037--3485104 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
3485027 TGACTTCTGT
*
3485037 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTCGC
* *
3485057 GTTGTGATTTTCCAAATTCGC
1 GTTGCGA-TTTACAAATTCGC
* *
3485078 GTTGCGATTTACATATTCAC
1 GTTGCGATTTACAAATTCGC
3485098 GTTGCGA
1 GTTGCGA
3485105 ATTTGGAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:3485841 original size:32 final size:31
Alignment explanation
Indices: 3485794--3485882 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
3485784 AATTAACCTG
*
3485794 AACTGAAATCGAAATTAACTAGAACAAAAAGCA
1 AACTG-AACCGAAATTAACT-GAACAAAAAGCA
**
3485827 AACTGAACCGAAATTAACCTGAACTGAAAGCA
1 AACTGAACCGAAATTAA-CTGAACAAAAAGCA
* **
3485859 ACCCAAACCGAAATTAACTTGAAC
1 AACTGAACCGAAATTAAC-TGAAC
3485883 TGAAAGAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
31 1 0.02
32 40 0.83
33 7 0.15
ACGTcount: A:0.51, C:0.21, G:0.12, T:0.16
Consensus pattern (31 bp):
AACTGAACCGAAATTAACTGAACAAAAAGCA
Found at i:3485848 original size:16 final size:16
Alignment explanation
Indices: 3485829--3485898 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
3485819 AAAAAGCAAA
*
3485829 CTGAACCGAAATTAAC
1 CTGAACCGAAAGTAAC
* *
3485845 CTGAACTGAAAGCAAC
1 CTGAACCGAAAGTAAC
** *
3485861 CCAAACCGAAATTAAC
1 CTGAACCGAAAGTAAC
* * *
3485877 TTGAACTGAAAGAAAC
1 CTGAACCGAAAGTAAC
3485893 CTGAAC
1 CTGAAC
3485899 TGAATTTTAA
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (16 bp):
CTGAACCGAAAGTAAC
Found at i:3485883 original size:32 final size:32
Alignment explanation
Indices: 3485803--3485893 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
3485793 GAACTGAAAT
* ** * **
3485803 CGAAATTAACTAGAACAAAAAGCAAACTGAAC
1 CGAAATTAACTTGAACTGAAAGCAACCCAAAC
*
3485835 CGAAATTAACCTGAACTGAAAGCAACCCAAAC
1 CGAAATTAACTTGAACTGAAAGCAACCCAAAC
*
3485867 CGAAATTAACTTGAACTGAAAGAAACC
1 CGAAATTAACTTGAACTGAAAGCAACC
3485894 TGAACTGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.14
Consensus pattern (32 bp):
CGAAATTAACTTGAACTGAAAGCAACCCAAAC
Found at i:3485953 original size:32 final size:33
Alignment explanation
Indices: 3485884--3485953 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
3485874 AACTTGAACT
* * *
3485884 GAAAGAAACCTGAACTGAATTTTAACCCGATCA
1 GAAAGAAACATGAACTGAAATTTAACCCGACCA
* * *
3485917 GAAAGTAACATGAACT-AAATTTAATCCGACCC
1 GAAAGAAACATGAACTGAAATTTAACCCGACCA
3485949 GAAAG
1 GAAAG
3485954 CAACCCGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (33 bp):
GAAAGAAACATGAACTGAAATTTAACCCGACCA
Found at i:3486335 original size:19 final size:19
Alignment explanation
Indices: 3486285--3486336 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3486275 TTTTTTAAAA
* *
3486285 TTTAATAAAAATATTAAGTT
1 TTTAATAAAAA-ATAAAATT
* **
3486305 TATAATTGAAAATAAAATT
1 TTTAATAAAAAATAAAATT
3486324 TTTAATAAAAAAT
1 TTTAATAAAAAAT
3486337 TATTTCTTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TTTAATAAAAAATAAAATT
Found at i:3486920 original size:3 final size:3
Alignment explanation
Indices: 3486912--3486963 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
3486902 GGTCTAAAAA
**
3486912 TAT TAT TA- TAT TAT TAT TAT CGT TAT T-T TAT TAT ATAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T-AT
3486957 TAT TAT T
1 TAT TAT T
3486964 TTTACATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3486931 original size:14 final size:14
Alignment explanation
Indices: 3486912--3486962 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
3486902 GGTCTAAAAA
3486912 TATTATTATATTAT
1 TATTATTATATTAT
3486926 TATTATCGT-TATT-T
1 TATTAT--TATATTAT
3486940 TATTA-TATATTAT
1 TATTATTATATTAT
3486953 TAATTATTAT
1 T-ATTATTAT
3486963 TTTTACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
11 1 0.03
12 4 0.13
13 2 0.06
14 16 0.52
15 7 0.23
16 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:3486959 original size:17 final size:17
Alignment explanation
Indices: 3486911--3486962 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
3486901 GGGTCTAAAA
3486911 ATATTATTATATTATTATT
1 ATATTATTA-ATTATTA-T
*
3486930 ATCGTTATT--TTATTAT
1 AT-ATTATTAATTATTAT
3486946 ATATTATTAATTATTAT
1 ATATTATTAATTATTAT
3486963 TTTTACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.18
16 3 0.11
17 13 0.46
19 2 0.07
20 5 0.18
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATTATTAATTATTAT
Found at i:3486962 original size:25 final size:25
Alignment explanation
Indices: 3486914--3486965 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3486904 TCTAAAAATA
*
3486914 TTATTATATTATTATTATCGTTATT
1 TTATTATATTATTATTATCATTATT
*
3486939 TTATTATA-TATTATTAATTATTATT
1 TTATTATATTATTATT-ATCATTATT
3486964 TT
1 TT
3486966 TACATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTATATTATTATTATCATTATT
Found at i:3488550 original size:30 final size:30
Alignment explanation
Indices: 3488516--3488576 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3488506 TCTATTTCAG
3488516 TCCTTTAACTTTCTGTTTTTATTATTTTAA
1 TCCTTTAACTTTCTGTTTTTATTATTTTAA
* * * *
3488546 TCCTTTAAGTTTTTGTTTTTTTTGTTTTAA
1 TCCTTTAACTTTCTGTTTTTATTATTTTAA
3488576 T
1 T
3488577 TATGTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.16, C:0.10, G:0.07, T:0.67
Consensus pattern (30 bp):
TCCTTTAACTTTCTGTTTTTATTATTTTAA
Found at i:3488907 original size:5 final size:5
Alignment explanation
Indices: 3488897--3488942 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
3488887 ATCTTTTCAC
* * * *
3488897 TTTTA TTTTA TTTTA TTTTA TTTTA GTTTA TATTA TCTTA TCTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
3488943 CTTTGCGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:3490827 original size:6 final size:6
Alignment explanation
Indices: 3490806--3490885 Score: 54
Period size: 6 Copynumber: 12.3 Consensus size: 6
3490796 AAAAAACATG
* * **
3490806 AAAATG AAAATA AAAATA AAAA-A ATAAATC AAAGGA CAAAATA AAAATAGA
1 AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA -AAAATA AAAAT--A
3490857 AAAATA GAAAATAA ATAAATA AAAATA AA
1 AAAATA -AAAAT-A A-AAATA AAAATA AA
3490886 TCGAAGGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
5 2 0.03
6 33 0.56
7 13 0.22
8 11 0.19
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:3490829 original size:14 final size:14
Alignment explanation
Indices: 3490812--3490885 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 14
3490802 CATGAAAATG
3490812 AAAATAAAAATAAA
1 AAAATAAAAATAAA
*
3490826 AAAATAAATCAA-AGGAC
1 AAAATAAA--AATA--AA
*
3490843 AAAATAAAAATAGA
1 AAAATAAAAATAAA
3490857 AAAATAGAAAATAAA
1 AAAATA-AAAATAAA
*
3490872 TAAATAAAAATAAA
1 AAAATAAAAATAAA
3490886 TCGAAGGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.45
15 15 0.31
16 3 0.06
17 9 0.18
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:3492137 original size:5 final size:5
Alignment explanation
Indices: 3492123--3492174 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
3492113 CCTGGACCAA
* *
3492123 AAAAT AAAAAT AAAAT AAAGT -TAAT AAAAT AAAAT AAAAT -AAAT AATAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
3492173 AA
1 AA
3492175 TATATTTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 23 0.59
6 10 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:3492153 original size:19 final size:19
Alignment explanation
Indices: 3492124--3492174 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3492114 CTGGACCAAA
*
3492124 AAATAAAAATAAAATAAAGT
1 AAAT-AAAATAAAATAAAAT
*
3492144 TAATAAAATAAAATAAAAT
1 AAATAAAATAAAATAAAAT
3492163 AAATAATAATAA
1 AAATAA-AATAA
3492175 TATATTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAT
Found at i:3492296 original size:60 final size:62
Alignment explanation
Indices: 3492230--3492348 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 62
3492220 TTTAAAAAGT
*
3492230 TTTCAAAACTATATATTATAT-AGTTGT-CAATAATG-TTTTAAAACTATATATTATATATGA
1 TTTCAAAACTATATATTATATAAGTTGTACAA-AATGATTTCAAAACTATATATTATATATGA
* *
3492290 TTTCAAAACTATATATTATATAAGTTTTACAAAATGATTTCAAAACTCTATATTATATA
1 TTTCAAAACTATATATTATATAAGTTGTACAAAATGATTTCAAAACTATATATTATATA
3492349 AGTTTTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 21 0.40
61 9 0.17
62 23 0.43
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (62 bp):
TTTCAAAACTATATATTATATAAGTTGTACAAAATGATTTCAAAACTATATATTATATATGA
Found at i:3492399 original size:39 final size:38
Alignment explanation
Indices: 3492290--3492563 Score: 391
Period size: 37 Copynumber: 7.2 Consensus size: 38
3492280 TTATATATGA
*
3492290 TTTC-AAAACTATATATTATATA-AGTTTTACAAAATGA
1 TTTCAAAAACTATATATTATATATAGTTTT-CAAAATGT
* *
3492327 TTTC-AAAACTCTATATTATATA-AGTTTTTAAAATGT
1 TTTCAAAAACTATATATTATATATAGTTTTCAAAATGT
3492363 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGT
1 TTTCAAAAACTATATATTATATATA-GTTTTCAAAATGT
3492402 TTTCAAAAACTATATATTATATATA-TTTTCAAAATGT
1 TTTCAAAAACTATATATTATATATAGTTTTCAAAATGT
3492439 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGT
1 TTTCAAAAACTATATATTATATATA-GTTTTCAAAATGT
3492478 TTTCAAAAACTATATATTATATATA-TTTTCAAAATGT
1 TTTCAAAAACTATATATTATATATAGTTTTCAAAATGT
* * *
3492515 TTTCAAAATCTATATAATATATACA-TTTTCAAAAATCGT
1 TTTCAAAAACTATATATTATATATAGTTTTC-AAAAT-GT
3492554 TTTCTAAAAA
1 TTTC-AAAAA
3492564 AATATTTTCA
Statistics
Matches: 220, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
36 10 0.05
37 120 0.55
38 6 0.03
39 80 0.36
40 4 0.02
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (38 bp):
TTTCAAAAACTATATATTATATATAGTTTTCAAAATGT
Found at i:3492418 original size:76 final size:76
Alignment explanation
Indices: 3492290--3492563 Score: 400
Period size: 76 Copynumber: 3.6 Consensus size: 76
3492280 TTATATATGA
* *
3492290 TTTC-AAAACTATATATTATATA-A-GTTTTACAAAATGATTTC-AAAACTCTATATTATATA-A
1 TTTCAAAAACTATATATTATATATATGTTTT-CAAAATGTTTTCAAAAACTATATATTATATATA
*
3492350 GTTTTTAAAATGT
65 -TTTTCAAAATGT
3492363 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
1 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
3492428 TTTCAAAATGT
66 TTTCAAAATGT
3492439 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
1 TTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
3492504 TTTCAAAATGT
66 TTTCAAAATGT
* **
3492515 TTTCAAAATCTATATA--ATATATACATTTTCAAAAATCGTTTTCTAAAAA
1 TTTCAAAAACTATATATTATATATATGTTTTC-AAAAT-GTTTTC-AAAAA
3492564 AATATTTTCA
Statistics
Matches: 187, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
73 4 0.02
74 30 0.16
75 17 0.09
76 130 0.70
77 6 0.03
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (76 bp):
TTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
TTTCAAAATGT
Found at i:3492598 original size:2 final size:2
Alignment explanation
Indices: 3492591--3492623 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3492581 TACTATACTA
3492591 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 A
3492624 ATAACAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3498803 original size:29 final size:29
Alignment explanation
Indices: 3498769--3498841 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
3498759 TTATTTTCTC
* *
3498769 ATAAATTATAATGAAGACCAAAA-TGTTTA
1 ATAAATTATAATAAAAACCAAAACT-TTTA
*
3498798 ATAAATTATAATAAAAACCAAAACTTTTT
1 ATAAATTATAATAAAAACCAAAACTTTTA
3498827 ATAAATTATAATAAA
1 ATAAATTATAATAAA
3498842 GGCCATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (29 bp):
ATAAATTATAATAAAAACCAAAACTTTTA
Found at i:3498880 original size:29 final size:28
Alignment explanation
Indices: 3498798--3498924 Score: 123
Period size: 29 Copynumber: 4.5 Consensus size: 28
3498788 AAAATGTTTA
* **
3498798 ATAAATTATAATAAAAACCAAAACTTTTT
1 ATAAATTACAAT-AAAGGCAAAACTTTTT
* * *
3498827 ATAAATTATAATAAAGGC--CATTTTTT
1 ATAAATTACAATAAAGGCAAAACTTTTT
*
3498853 ATAAATTACAATAATGGTCAAAACTTTTT
1 ATAAATTACAATAAAGG-CAAAACTTTTT
* * *
3498882 ATAAATTACAAAAAAGGACAAAACTTATC
1 ATAAATTACAATAAAGG-CAAAACTTTTT
3498911 ATAAATTACAATAA
1 ATAAATTACAATAA
3498925 TAACCTATAG
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 21 0.26
27 1 0.01
28 4 0.05
29 55 0.68
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (28 bp):
ATAAATTACAATAAAGGCAAAACTTTTT
Found at i:3498970 original size:28 final size:28
Alignment explanation
Indices: 3498913--3498982 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3498903 AACTTATCAT
3498913 AAATTACAATAATAACCTATAGTTTCTAC
1 AAATTACAATAA-AACCTATAGTTTCTAC
* *
3498942 AAATTACAATAAAACCTTGTA-TTTTTAC
1 AAATTACAATAAAACC-TATAGTTTCTAC
3498970 AAATTACAATAAA
1 AAATTACAATAAA
3498983 GCTACATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (28 bp):
AAATTACAATAAAACCTATAGTTTCTAC
Found at i:3499795 original size:33 final size:33
Alignment explanation
Indices: 3499753--3499828 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
3499743 AATATCTATC
3499753 AGCTTTAATAAGAACATCCTTATCGGAGACTTT
1 AGCTTTAATAAGAACATCCTTATCGGAGACTTT
3499786 AGCTTTAATAAGAACATCCTTATCGGAGACTTT
1 AGCTTTAATAAGAACATCCTTATCGGAGACTTT
3499819 AGCTTTAATA
1 AGCTTTAATA
3499829 TAAATCATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (33 bp):
AGCTTTAATAAGAACATCCTTATCGGAGACTTT
Found at i:3500814 original size:20 final size:22
Alignment explanation
Indices: 3500774--3500823 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
3500764 TTTCCAAAAT
*
3500774 AATTTAAATATTTTTTAAATAA
1 AATTTTAATATTTTTTAAATAA
3500796 AATTTTAATA-TTTTT-AATAA
1 AATTTTAATATTTTTTAAATAA
*
3500816 ATTTTTAA
1 AATTTTAA
3500824 AAGTTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
21 5 0.19
22 9 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTAATATTTTTTAAATAA
Found at i:3500830 original size:20 final size:21
Alignment explanation
Indices: 3500786--3500835 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3500776 TTTAAATATT
*
3500786 TTTTAAATAAAATTTTAATA-
1 TTTTAAATAAAATTTTAAAAG
* *
3500806 TTTTTAATAAATTTTTAAAAG
1 TTTTAAATAAAATTTTAAAAG
3500827 TTTTCAAAT
1 TTTT-AAAT
3500836 GATGTCGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.71
21 4 0.17
22 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTAAATAAAATTTTAAAAG
Found at i:3500896 original size:16 final size:17
Alignment explanation
Indices: 3500855--3500896 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
3500845 TCTCACATCA
3500855 ATATTTTTTAATATATT
1 ATATTTTTTAATATATT
3500872 ATATCTTTTTAATA-ATAT
1 ATAT-TTTTTAATATAT-T
3500890 ATATTTT
1 ATATTTT
3500897 AAAAATATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTTTTAATATATT
Found at i:3500898 original size:15 final size:15
Alignment explanation
Indices: 3500855--3500904 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
3500845 TCTCACATCA
3500855 ATATTTTTTAATATATT
1 ATATTTTTTAATA-A-T
3500872 ATATCTTTTTAATAAT
1 ATAT-TTTTTAATAAT
* *
3500888 ATATATTTTAAAAAT
1 ATATTTTTTAATAAT
3500903 AT
1 AT
3500905 TGTTAGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 11 0.37
16 5 0.17
17 5 0.17
18 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTTTAATAAT
Found at i:3501322 original size:30 final size:30
Alignment explanation
Indices: 3501288--3501355 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
3501278 TTAAATTTTA
* *
3501288 AATATTTTTAATACTATAGAATAATTATGT
1 AATATTTTTAATACTATAAAATAATTATAT
* * *
3501318 AATATTTTTATTATTTTAAAATAATTATAT
1 AATATTTTTAATACTATAAAATAATTATAT
3501348 AATATTTT
1 AATATTTT
3501356 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
AATATTTTTAATACTATAAAATAATTATAT
Found at i:3502953 original size:39 final size:39
Alignment explanation
Indices: 3502880--3502996 Score: 125
Period size: 39 Copynumber: 3.0 Consensus size: 39
3502870 TAAAATTTTT
* * *
3502880 ATTCATAATTT-TCAAATTATTTCAC-TCTATCATTCTAA
1 ATTCATAATTTCTTAAATTATTCCACAT-TAACATTCTAA
3502918 ATTCATAATTTCTTAAATT-TTGCCACCA-TAACATTCTAA
1 ATTCATAATTTCTTAAATTATT-CCA-CATTAACATTCTAA
* * *
3502957 ATTCTTACTTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTCATAATTTCTTAAATTATTCCACATTAACATTCTAA
3502996 A
1 A
3502997 CTATTTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
38 15 0.22
39 49 0.73
40 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (39 bp):
ATTCATAATTTCTTAAATTATTCCACATTAACATTCTAA
Found at i:3504658 original size:26 final size:26
Alignment explanation
Indices: 3504602--3504659 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
3504592 GAATTTATAC
* *
3504602 ATTTATTAAAAAAAATTATATATTTAA
1 ATTT-TTAAAAAAAATTATAAATTCAA
*
3504629 ATTTTTAAAAAAAA-TACTAAATTCAT
1 ATTTTTAAAAAAAATTA-TAAATTCAA
3504655 ATTTT
1 ATTTT
3504660 AGCTAAAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.78
27 4 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTTAAAAAAAATTATAAATTCAA
Found at i:3509223 original size:57 final size:57
Alignment explanation
Indices: 3509160--3509328 Score: 293
Period size: 57 Copynumber: 3.0 Consensus size: 57
3509150 GAAAAGAGTT
* * * *
3509160 AAAAAATAGAGTTTGGTATAAGCACATAGCCTATAAATAACCAGTTTCAAGCCTATA
1 AAAAAATAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTATA
3509217 AAAAAATAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTATA
1 AAAAAATAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTATA
*
3509274 AAAAAGTAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTA
1 AAAAAATAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTA
3509329 CATTTAATTA
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 107 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (57 bp):
AAAAAATAGAGTTTGGCATTAGTACACAGCCTATAAATAACCAGTTTCAAGCCTATA
Found at i:3511401 original size:218 final size:218
Alignment explanation
Indices: 3511023--3511459 Score: 874
Period size: 218 Copynumber: 2.0 Consensus size: 218
3511013 TAATAGATCA
3511023 GTTAAACATGGATGGATTTGTTTCATGGTCCAATTGAATTGAATTAGGCTAAAAGAAAGTAGATT
1 GTTAAACATGGATGGATTTGTTTCATGGTCCAATTGAATTGAATTAGGCTAAAAGAAAGTAGATT
3511088 TTCTTGATCATGTTTTCTTTCAACCCTTTTATTTCATTGTCTCTTTTTCTCTTTTTTTCTGTATT
66 TTCTTGATCATGTTTTCTTTCAACCCTTTTATTTCATTGTCTCTTTTTCTCTTTTTTTCTGTATT
3511153 GATTTTCTAGTATTTGCCTTTTCCAAAAAAAAAATCTGGTATTTGAATATTTTTGTGAATTTGAT
131 GATTTTCTAGTATTTGCCTTTTCCAAAAAAAAAATCTGGTATTTGAATATTTTTGTGAATTTGAT
3511218 ATTTGCTCTTTTCCTTAGTTGAG
196 ATTTGCTCTTTTCCTTAGTTGAG
3511241 GTTAAACATGGATGGATTTGTTTCATGGTCCAATTGAATTGAATTAGGCTAAAAGAAAGTAGATT
1 GTTAAACATGGATGGATTTGTTTCATGGTCCAATTGAATTGAATTAGGCTAAAAGAAAGTAGATT
3511306 TTCTTGATCATGTTTTCTTTCAACCCTTTTATTTCATTGTCTCTTTTTCTCTTTTTTTCTGTATT
66 TTCTTGATCATGTTTTCTTTCAACCCTTTTATTTCATTGTCTCTTTTTCTCTTTTTTTCTGTATT
3511371 GATTTTCTAGTATTTGCCTTTTCCAAAAAAAAAATCTGGTATTTGAATATTTTTGTGAATTTGAT
131 GATTTTCTAGTATTTGCCTTTTCCAAAAAAAAAATCTGGTATTTGAATATTTTTGTGAATTTGAT
3511436 ATTTGCTCTTTTCCTTAGTTGAG
196 ATTTGCTCTTTTCCTTAGTTGAG
3511459 G
1 G
3511460 CTTGAAGGAG
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 219 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (218 bp):
GTTAAACATGGATGGATTTGTTTCATGGTCCAATTGAATTGAATTAGGCTAAAAGAAAGTAGATT
TTCTTGATCATGTTTTCTTTCAACCCTTTTATTTCATTGTCTCTTTTTCTCTTTTTTTCTGTATT
GATTTTCTAGTATTTGCCTTTTCCAAAAAAAAAATCTGGTATTTGAATATTTTTGTGAATTTGAT
ATTTGCTCTTTTCCTTAGTTGAG
Found at i:3513478 original size:16 final size:17
Alignment explanation
Indices: 3513459--3513503 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
3513449 GTTTCTTTAC
3513459 ATTTTAATATTTCAA-A
1 ATTTTAATATTTCAATA
3513475 ATTTTCAA-ATTTCAATA
1 ATTTT-AATATTTCAATA
*
3513492 ATTTAAATATTT
1 ATTTTAATATTT
3513504 TTATTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTAATATTTCAATA
Found at i:3515943 original size:24 final size:24
Alignment explanation
Indices: 3515916--3515962 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3515906 CTTTTATATA
*
3515916 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
3515940 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
3515963 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:3520830 original size:17 final size:17
Alignment explanation
Indices: 3520758--3520847 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
3520748 AAAATGGTTA
* *
3520758 CAACATAAAAAGGAGTTG
1 CAACAT-AAAATGAGGTG
* *
3520776 CAACCTAAAATGTGGTG
1 CAACATAAAATGAGGTG
* * * *
3520793 -AACTTGAAAAAGTGGTA
1 CAACAT-AAAATGAGGTG
3520810 CAACATAAAATGAGGTG
1 CAACATAAAATGAGGTG
3520827 CAACCATAAAAT-AGGTTG
1 CAA-CATAAAATGAGG-TG
3520845 CAA
1 CAA
3520848 TTTAAAATGT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.07
17 31 0.54
18 22 0.39
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (17 bp):
CAACATAAAATGAGGTG
Found at i:3520836 original size:18 final size:18
Alignment explanation
Indices: 3520813--3520847 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3520803 AGTGGTACAA
3520813 CATAAAATGAGG-TGCAAC
1 CATAAAAT-AGGTTGCAAC
3520831 CATAAAATAGGTTGCAA
1 CATAAAATAGGTTGCAA
3520848 TTTAAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (18 bp):
CATAAAATAGGTTGCAAC
Found at i:3521603 original size:32 final size:32
Alignment explanation
Indices: 3521567--3521643 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
3521557 CGGGGCCACG
*
3521567 GGGCCTACCTAAGAACAT-ATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
** *
3521599 GGGCCTACCCGAG-AATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
*
3521630 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3521644 GTCACATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
30 2 0.06
31 23 0.64
32 11 0.31
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:3525902 original size:25 final size:25
Alignment explanation
Indices: 3525869--3525920 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3525859 ACTTTCAATT
3525869 TTTGTGATTTCTGTGAAAACATACA
1 TTTGTGATTTCTGTGAAAACATACA
3525894 TTTGTGATTTCTGTGAAAACATACA
1 TTTGTGATTTCTGTGAAAACATACA
3525919 TT
1 TT
3525921 CTTCGATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTGTGATTTCTGTGAAAACATACA
Found at i:3526839 original size:13 final size:14
Alignment explanation
Indices: 3526817--3526845 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3526807 CAAGTAATTT
3526817 AAAAAGATATATAC
1 AAAAAGATATATAC
3526831 AAAAA-ATATATAC
1 AAAAAGATATATAC
3526844 AA
1 AA
3526846 CAACATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAAAGATATATAC
Found at i:3526918 original size:18 final size:17
Alignment explanation
Indices: 3526895--3526930 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
3526885 ATGAAAATTG
3526895 AAATTAATAAAATACAAT
1 AAATTAATAAAATA-AAT
3526913 AAATTAATAAAATAAAT
1 AAATTAATAAAATAAAT
3526930 A
1 A
3526931 CACAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATTAATAAAATAAAT
Found at i:3533299 original size:65 final size:64
Alignment explanation
Indices: 3533189--3533332 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
3533179 ATAAGACTTA
* * *
3533189 GTGCATCGGTACACTAATTACATTCGATGTTTTAAAAAAGCCAAGAGTGCATTGATGCATGGCAT
1 GTGCATCGGTACA-TAAATACATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGGC-T
3533254 -
64 C
* * **
3533254 GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTC
1 GTGCATCGGTACAT-AAATACATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGGCTC
3533319 GTGCATCGGTACAT
1 GTGCATCGGTACAT
3533333 CCCTTTGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 2 0.03
65 68 0.97
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAATACATTCGATGTTTCAAAAAAGCCAAGAGTGCATCGATGCATGGCTC
Found at i:3535508 original size:15 final size:15
Alignment explanation
Indices: 3535476--3535506 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3535466 AAAACATCAA
3535476 TTAAAACAATATTTT
1 TTAAAACAATATTTT
3535491 TTAAAA-AATATTTT
1 TTAAAACAATATTTT
3535505 TT
1 TT
3535507 TATTTCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAAACAATATTTT
Found at i:3535941 original size:23 final size:23
Alignment explanation
Indices: 3535911--3535978 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
3535901 ATGCACAACA
3535911 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * *
3535934 GAGTGCATCGGTGCACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
* *
3535956 G-GTGTATTGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
3535978 G
1 G
3535979 GATGCGTCGG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 14 0.39
22 4 0.11
23 18 0.50
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:3541815 original size:65 final size:65
Alignment explanation
Indices: 3541743--3541882 Score: 176
Period size: 65 Copynumber: 2.2 Consensus size: 65
3541733 CTAGGGGTGC
* *
3541743 ATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATTCATGGTCCGTG
1 ATCGGTACA-TAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTCCGTG
3541807 T
65 T
* * ** *
3541808 ATCGGTACATAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGG-CTTGTG
1 ATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTC-CGTG
*
3541872 C
65 T
3541873 ATCGGTACAT
1 ATCGGTACAT
3541883 CCCTTTGGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
64 2 0.03
65 63 0.97
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (65 bp):
ATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTCCGTGT
Found at i:3542551 original size:21 final size:20
Alignment explanation
Indices: 3542504--3542618 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
3542494 TCTTTTAAGG
* *
3542504 GAAGGGATCAATCCTTTTCAT
1 GAAGGGATCGATCCTTTT-GT
3542525 CG-AGGGATCGATCCTTTTGGT
1 -GAAGGGATCGATCCTTTT-GT
*
3542546 GAAGGGATCGATTCTTTT-T
1 GAAGGGATCGATCCTTTTGT
* * * *
3542565 CAAGGGGGTTGATCCTTTGGT
1 GAA-GGGATCGATCCTTTTGT
* *
3542586 CAAGGGATTGATCCTTTTGT
1 GAAGGGATCGATCCTTTTGT
* *
3542606 TAAGGAATCGATC
1 GAAGGGATCGATC
3542619 ATTTGAGCAA
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.04
20 37 0.49
21 35 0.46
22 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (20 bp):
GAAGGGATCGATCCTTTTGT
Found at i:3543893 original size:158 final size:158
Alignment explanation
Indices: 3543700--3544066 Score: 511
Period size: 158 Copynumber: 2.3 Consensus size: 158
3543690 CTTGATTTCA
* * * * **
3543700 TTATTTCTTCAATTCCTCCTTCATTTTAAGTCCATTTTTTACCAAATTTGATCCACATGTTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTTACCAAATTTGAGCCACATACTCCTA
* *
3543765 AACCATAGT-AGAATGCATGTGTACTTTCAATTACTCTTTTTGATAACAAATTTTTTATTTTTCA
66 AACCATAGTCA-AATACATGTGTACTTTCAATTACTATTTTTGATAACAAATTTTTTATTTTTCA
* *
3543829 ATTTAGTCCTTCAATTTTTCATAATCTCC
130 ATTTAATCCTTCAATTTTCCATAATCTCC
* *
3543858 TTATTTCTTCAATTCGTCATTTATTTTAAGTCCATTTTTTACCAAACTTGAGCCACATACTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTTACCAAATTTGAGCCACATACTCCTA
* **
3543923 TACCATAGTCAAATACATGTGTACTTTCAATTACTATTTTTGATAACAAATTTTTTATTTTTTTA
66 AACCATAGTCAAATACATGTGTACTTTCAATTACTATTTTTGATAACAAATTTTTTATTTTTCAA
*
3543988 TTTAATCCTTCAATTTTCCATAATCTTC
131 TTTAATCCTTCAATTTTCCATAATCTCC
* * ** **
3544016 TTATTCCTTCAATTTATGGTTTATTTTAAGTCTTTTGTTTTACCAAATTTG
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCATT-TTTTACCAAATTTG
3544067 TCTCATATAC
Statistics
Matches: 184, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
158 170 0.92
159 14 0.08
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (158 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTTACCAAATTTGAGCCACATACTCCTA
AACCATAGTCAAATACATGTGTACTTTCAATTACTATTTTTGATAACAAATTTTTTATTTTTCAA
TTTAATCCTTCAATTTTCCATAATCTCC
Found at i:3546560 original size:24 final size:24
Alignment explanation
Indices: 3546526--3546588 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3546516 AAAAAATTAG
* *
3546526 AAGTTCGATTGAAGGCTAAAATTT
1 AAGTTCAATTGAAGCCTAAAATTT
3546550 AAGTTCAATTGAAGCCTAAAATTT
1 AAGTTCAATTGAAGCCTAAAATTT
* *
3546574 GAGCTCAATTGAAGC
1 AAGTTCAATTGAAGC
3546589 GAAAGAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (24 bp):
AAGTTCAATTGAAGCCTAAAATTT
Found at i:3551120 original size:182 final size:182
Alignment explanation
Indices: 3550813--3551478 Score: 955
Period size: 182 Copynumber: 3.7 Consensus size: 182
3550803 TGTCGGTTTA
*
3550813 TGTCGATACTTTATAA-AACTGTATCGATCCAC-ATCAATATAACAGGTAAAAATATGACAAAAC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAAT-GATATAACAGGTAAAAATATGACAAAAC
* * * *
3550876 CGGTCTCGAAAAGATAAAACCGGTA-A-AGCGATATCGGCTATATTGAAAGTGTCGATACTTTAA
64 CGGTCTCTAAAGGACAAAACCGGTATAGAGCG--ATCGGATATATTGAAAGTGTCGATACTTTAA
* *
3550939 TATAAGTATTGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGAGCCTATAAAG
127 TATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGAGCCTATAAAG
* * *
3550995 TGTCGATATTTTATAATAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCG
* *
3551060 GTCTCTAAAGGACAAAACCGGTATAGAGCGATCAGATATATTGAAAGCGTCGATACTTTAATATA
66 GTCTCTAAAGGACAAAACCGGTATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATATA
*
3551125 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTA-ACGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGA-GCCTATAAAG
* * *
3551177 TGTCGATATTTTATAACAATGTATCTATCCACAATGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCG
** * * *
3551242 GTCTCTAAAGGACAAAACTAGTATAGAGCGACCGAATATATTGAAAGTGTTGATACTTTAATATA
66 GTCTCTAAAGGACAAAACCGGTATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATATA
*
3551307 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCCT-TAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGAG-CCTATAAAG
* *
3551359 TGTCGATACTTTATAACAATGTATCGATCCAAAACGATATAACAGG--------TGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCG
*
3551416 GTCTCTAAAGGACAAAACCGGTATAGAGCGATCGGATATATTTAAAGTGTCGATACTTTAATA
66 GTCTCTAAAGGACAAAACCGGTATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATA
3551479 AGTACGCGTA
Statistics
Matches: 443, Mismatches: 34, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
174 67 0.15
181 1 0.00
182 363 0.82
183 8 0.02
184 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCG
GTCTCTAAAGGACAAAACCGGTATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGAGCCTATAAAG
Found at i:3553777 original size:21 final size:21
Alignment explanation
Indices: 3553753--3553796 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3553743 AAGACAATCA
3553753 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
3553774 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3553795 AG
1 AG
3553797 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3553872 original size:33 final size:33
Alignment explanation
Indices: 3553830--3553929 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
3553820 AAATAAATGG
3553830 AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
*
3553863 AGTGGTGAAAGAAGTTTAA-GTGTTGAGGGATGA
1 AGTGGTGAAAGAAG-TTAAGGTGTTGAGGGGTGA
* *
3553896 AGTGGTGAAAGAAGTTGAGGTGTTGAGTGGTGA
1 AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
3553929 A
1 A
3553930 CTTAAGACGG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.05
33 54 0.89
34 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.43, T:0.26
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
Found at i:3554132 original size:18 final size:18
Alignment explanation
Indices: 3554109--3554144 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3554099 GAAAAAATAT
3554109 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3554127 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3554145 AAAATGATGA
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:0.56, C:0.00, G:0.39, T:0.06
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3555727 original size:19 final size:19
Alignment explanation
Indices: 3555703--3555751 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3555693 AATGTAGGGT
3555703 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
**
3555722 TAATTTTGTATACTATTTA
1 TAATTTTGTATAAGATTTA
3555741 TAATTTTGTAT
1 TAATTTTGTAT
3555752 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3556091 original size:15 final size:15
Alignment explanation
Indices: 3556067--3556101 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3556057 AGTATGGTTC
3556067 CCAAACGTAAAGTTT
1 CCAAACGTAAAGTTT
*
3556082 CCAAATGTAAAGTTT
1 CCAAACGTAAAGTTT
3556097 CCAAA
1 CCAAA
3556102 AAATAGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (15 bp):
CCAAACGTAAAGTTT
Found at i:3556474 original size:200 final size:199
Alignment explanation
Indices: 3556118--3557098 Score: 1033
Period size: 200 Copynumber: 4.8 Consensus size: 199
3556108 GTAAACATAT
*
3556118 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
3556183 GGTAATTTTATAATATAACC-AGTATAAATATACCGGTTTTATGTGAGAATAAGTCTACATAATG
66 GGTAAATTTACAATGTAACCGA-TATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATA
* * * * *
3556247 TATCGACACTTTTGAAATTGTTGTCGATACTTTTTTTCCAGAATGAATGCCCAAAATGGTGAACG
130 TATCGACACTTTTGAATTTG-TGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACG
3556312 CATAAA
194 CATAAA
* * *
3556318 GTGTAGATACATTTATAAAAAATATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
3556383 GGTAAATTTACAATGTAATCGAAATAACTATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
* * *
3556448 ATCGACACTTATGGAATTTGTGTCGATACTGTTTGTCAAGAAGGAATGCCCAAAAGGGTGCACGC
131 ATCGACACTT-TTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACGC
3556513 ATAAA
195 ATAAA
* * **
3556518 GTGTCGATACATTTTTAAAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCGAA
1 GTGTCGATACATTTATAAAAAGTATCGAT-C----CCAAAAA----C-AT--C---G--A---AA
* ** *
3556583 CCCATAATTATAATGTAATAGGTAATTTTGTAATGTAACTTG-TATAAATATACCAGG-TTTATG
46 CCCATAATTATAATGTAATAGGTAAATTTACAATGTAAC-CGATATAAATATACC-GGTTTTATG
* * * *
3556646 TGAGAATAGGTCTACATAA-AGTATCGACACTTTTTAATTATGTGTCGATACATTTTGTCCATAA
109 AGAGAATAGGTCTACATAATA-TATCGACACTTTTGAATT-TGTGTCGATACTTTTTGTCCAGAA
* *
3556710 TGAATGCCCAAAAAAATGGTGCACGCATAAA
172 GGAATGCCC---AAAAGGGTGCACGCATAAA
* * *
3556741 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * * * *
3556806 AGT-AATTTGTCAATGTAACCGGTATAAATACACCAGTTTTATGCGAGAATAGGTCTAGAAAATG
66 GGTAAATTT-ACAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATA
* * *
3556870 TATCGACACTTCTGGAATTTGTGTCGATACTTTTTGTCCAAAAGGAATG-CCAAAAGGGTGCACC
130 TATCGACACTT-TTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACG
*
3556934 CATTAA
194 CATAAA
* * * * *
3556940 GTATCAATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
3557005 GGTAAATTTCCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTC-AGCATAA-A
66 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATA
* *
3557068 GTATCGACAATTGTTAAATTTGTGTCGATAC
130 -TATCGACACTT-TTGAATTTGTGTCGATAC
3557099 CATTTTAAAA
Statistics
Matches: 652, Mismatches: 92, Indels: 75
0.80 0.11 0.09
Matches are distributed among these distances:
198 1 0.00
199 144 0.22
200 199 0.31
201 9 0.01
202 8 0.01
203 102 0.16
204 5 0.01
205 4 0.01
206 1 0.00
208 1 0.00
209 1 0.00
210 2 0.00
211 1 0.00
212 1 0.00
213 2 0.00
215 1 0.00
217 1 0.00
218 4 0.01
219 6 0.01
220 110 0.17
221 3 0.00
222 1 0.00
223 45 0.07
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
ATCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACGCA
TAAA
Found at i:3556539 original size:21 final size:21
Alignment explanation
Indices: 3556515--3556567 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3556505 GTGCACGCAT
3556515 AAAGTGTCGATACATTTTTAA
1 AAAGTGTCGATACATTTTTAA
3556536 AAAGTGTCGATACATTTTTAA
1 AAAGTGTCGATACATTTTTAA
3556557 AAAGTGTCGAT
1 AAAGTGTCGAT
3556568 CCCAGAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
AAAGTGTCGATACATTTTTAA
Found at i:3556607 original size:220 final size:213
Alignment explanation
Indices: 3556315--3556968 Score: 650
Period size: 220 Copynumber: 3.1 Consensus size: 213
3556305 GTGAACGCAT
* *
3556315 AAAGTGTAGATACATTTATAAAAAATATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTAT-AAAAAT-TCGATCCCAGAGACATCG-AACCCATAATTATAATGTA
* * *
3556380 ATAGGTAAATTTACAATGTAATCGAAATAACTATACCGGTTTTATGAGAGAATAGGTCTACATAA
63 ATAGGT-AATTTTCAATGTAATCG-TATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAA
3556445 TATATCGACACTTATGGAATTTGTGTCGATACTGTTTGTCAAGAAGGAATGCCCAAAAGGGTGCA
126 TATATCGACACTT-TGGAATTTGTGTCGATACT-TTTGTCAA-AAGGAATGCCCAAAAGGGTGCA
3556510 CGCATAAAGTGTCGATACATTTTTAA
188 CGCATAAAGTGTCGATACATTTTTAA
*
3556536 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCGAACCCATAATTATAATGTAA
1 AAAGTGTCGATACATTTATAAAAA-T-TCGATCCCAGAGACATCGAACCCATAATTATAATGTAA
* * *
3556601 TAGGTAATTTTGTAATGTAACTTGTATAAATATACCAGG-TTTATGTGAGAATAGGTCTACATAA
64 TAGGTAATTTT-CAATGTAA-TCGTATAAATATACC-GGTTTTATGAGAGAATAGGTCTACATAA
** * * *
3556665 -AGTATCGACACTTTTTAATTATGTGTCGATACATTTTGTCCATAATGAATGCCCAAAAAAATGG
126 TA-TATCGACACTTTGGAATT-TGTGTCGATAC-TTTTGT-CAAAAGGAATGCCC---AAAAGGG
*
3556729 TGCACGCATAAAGTGTCGATACATTTATAA
184 TGCACGCATAAAGTGTCGATACATTTTTAA
* * *
3556759 AAA-----G---------T----A-TCGATCCCAGAAATATCGAAACCCATGATTATAATGTAAT
1 AAAGTGTCGATACATTTATAAAAATTCGATCCCAGAGACATCG-AACCCATAATTATAATGTAAT
* * * * * * * *
3556805 AAGTAATTTGTCAATGTAACCGGTATAAATACACCAGTTTTATGCGAGAATAGGTCTAGAAAATG
65 AGGTAATTT-TCAATGTAATC-GTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATA
*
3556870 TATCGACACTTCTGGAATTTGTGTCGATACTTTTTGTCCAAAAGGAATG-CCAAAAGGGTGCACC
128 TATCGACACTT-TGGAATTTGTGTCGATAC-TTTTGT-CAAAAGGAATGCCCAAAAGGGTGCACG
* * *
3556934 CATTAAGTATCAATACATTTTTAA
190 CATAAAGTGTCGATACATTTTTAA
3556958 AAAGTGTCGAT
1 AAAGTGTCGAT
3556969 CCCAAAAACA
Statistics
Matches: 369, Mismatches: 40, Indels: 63
0.78 0.08 0.13
Matches are distributed among these distances:
199 34 0.09
202 19 0.05
203 107 0.29
204 7 0.02
205 1 0.00
209 1 0.00
218 1 0.00
219 11 0.03
220 108 0.29
221 42 0.11
223 38 0.10
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (213 bp):
AAAGTGTCGATACATTTATAAAAATTCGATCCCAGAGACATCGAACCCATAATTATAATGTAATA
GGTAATTTTCAATGTAATCGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATATAT
CGACACTTTGGAATTTGTGTCGATACTTTTGTCAAAAGGAATGCCCAAAAGGGTGCACGCATAAA
GTGTCGATACATTTTTAA
Found at i:3556895 original size:203 final size:198
Alignment explanation
Indices: 3556536--3557104 Score: 716
Period size: 199 Copynumber: 2.8 Consensus size: 198
3556526 ACATTTTTAA
*
3556536 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCG-AACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
** * * *
3556600 ATAGGTAATTTTGT-AATGTAACTTGTATAAATATACCAGGTTTATGTGAGAATAGGTCTACATA
66 ATAGGTAA-TTTGTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTAGATA
* * * *
3556664 AAGTATCGACACTTTTTAATTATGTGTCGATACATTTTGTCCATAATGAATGCCCAAAAAAATGG
130 AAGTATCGACACTTTTAAATT-TGTGTCGATACATTTTGTCCAAAAGGAATG-CC---AAAAGGG
*
3556729 TGCACGCAT
190 TGCACCCAT
* * * *
3556738 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATGATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* * *
3556803 ATAAGTAATTTGTCAATGTAACCGGTATAAATACACCAGTTTTATGCGAGAATAGGTCTAGA-AA
66 ATAGGTAATTTGTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTAGATAA
** *
3556867 ATGTATCGACACTTCTGGAATTTGTGTCGATACTTTTTGTCCAAAAGGAATGCCAAAAGGGTGCA
131 A-GTATCGACACTT-TTAAATTTGTGTCGATACATTTTGTCCAAAAGGAATGCCAAAAGGGTGCA
3556932 CCCAT
194 CCCAT
* * * * *
3556937 TAAGTATCAATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
* * * *
3557002 ATAGGTAAATTT-CCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAAGTC-AGCAT
66 ATAGGT-AATTTGTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTAG-AT
*
3557065 AAAGTATCGACAATTGTTAAATTTGTGTCGATACCATTTT
129 AAAGTATCGACACTT-TTAAATTTGTGTCGATA-CATTTT
3557105 AAAAATCACG
Statistics
Matches: 319, Mismatches: 40, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
198 2 0.01
199 142 0.45
200 13 0.04
202 51 0.16
203 106 0.33
204 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (198 bp):
AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
ATAGGTAATTTGTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTAGATAA
AGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCAAAAGGAATGCCAAAAGGGTGCACC
CAT
Found at i:3558614 original size:6 final size:6
Alignment explanation
Indices: 3558562--3558626 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
3558552 CAAGAGATCA
* * * ** *
3558562 ATGAAG ATGAAG ATGAAG ATGAAC ATGATA ATGATG ATGATG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
*
3558610 ATGATG ATTATG ATGAT
1 ATGATG ATGATG ATGAT
3558627 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.42, C:0.02, G:0.28, T:0.29
Consensus pattern (6 bp):
ATGATG
Found at i:3559960 original size:18 final size:18
Alignment explanation
Indices: 3559939--3559991 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3559929 ATGTAATTGG
* *
3559939 AGTTTGAATTTAAATTTT
1 AGTTTGAATTTAAATATC
3559957 AGTTTGAATTTAAATATC
1 AGTTTGAATTTAAATATC
* *
3559975 AGTTTGAGTTTCAATAT
1 AGTTTGAATTTAAATAT
3559992 AAATTTTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (18 bp):
AGTTTGAATTTAAATATC
Found at i:3561673 original size:200 final size:199
Alignment explanation
Indices: 3561330--3562298 Score: 1286
Period size: 200 Copynumber: 4.8 Consensus size: 199
3561320 TAAAGTGTCC
* * * * *
3561330 CATAAAGTGTCGATACATGTTTAAAAAGTATTGATCCCAAAAACATCAAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * *
3561395 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTGTTT-TGAGAAAATAGATATAC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGT-TTTATGAGAGAATAGGTCTAC
*
3561459 ATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAATGTGT
130 ATAATGTATCGACACTT-TGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAATGGGT
3561524 TGCACG
194 TGCACG
*
3561530 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* ** * * *
3561595 GTAATAGGTAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA
* * * *
3561660 TAATGTGTCGACACTTTTGAATTTTGTGTCGATACTTTTTGTCCATAATGATTGCCCAAAAT-GG
131 TAATGTATCGACACTTTGGAA-TTTGTGTCGATACTTTTTGTCCAAAATGAATG-CC-AAATGGG
*
3561724 -TGAACG
193 TTGCACG
* ** * *
3561730 TATAAAGTGTCGATACATTTACAAAAAGTATCGATCCTAGAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* *
3561795 GTAATAGGTAAATTTACAATGTAACCAGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA
*
3561860 TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
131 TAATGTATCGACACTT-TGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAATGGGTT
3561925 GCACG
195 GCACG
*
3561930 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGAATAATTATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACC-CATAATTATAA
* * * * * **
3561995 TTTAATAGGTAAATTTACAATGTAACCAGTATAAATTTACCGGTTTTATGAGAAAATAAGTGAAC
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAC
* * * * * *
3562060 ATAATGTATCAACACGTTT-TAGATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGGG
130 ATAATGTATCGACAC-TTTGGA-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAATGGG
* *
3562124 GTGCAGG
193 TTGCACG
* * * ** *
3562131 CAGAAAGTGTCAATACA-TTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * *
3562195 GTAATAGGTAAATTTACAATGTAACTGGTATAAATATACTGGTTTTATGAGAGAATAAGT-TAAC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT-AC
* *
3562259 ATAATGTATCGACACTTT-TAAGTTTGTGTCGATACATTTT
130 ATAATGTATCGACACTTTGGAA-TTTGTGTCGATACTTTTT
3562299 AAATAACGTA
Statistics
Matches: 681, Mismatches: 76, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
197 1 0.00
198 26 0.04
199 92 0.14
200 408 0.60
201 148 0.22
202 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA
TAATGTATCGACACTTTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAATGGGTTG
CACG
Found at i:3563927 original size:19 final size:19
Alignment explanation
Indices: 3563903--3563951 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3563893 AATGTAAGGT
3563903 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
** *
3563922 TAATTTTACATATGATTTA
1 TAATTTTGTATAAGATTTA
3563941 TAATTTTGTAT
1 TAATTTTGTAT
3563952 GTGAATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3566810 original size:200 final size:198
Alignment explanation
Indices: 3566427--3566843 Score: 610
Period size: 201 Copynumber: 2.1 Consensus size: 198
3566417 ACCTAAATAT
3566427 GTGTCGATACATTT-TCTAAAAGTATCGACCCAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACATTTAT-TAAAAGTATCGACCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * *
3566491 GGTAAATTAACAATGTAACTGGTATAAATATACCGATTAATTAGAAAACAGGTCAACATAATGTA
65 GGTAAATTAACAATGTAACCGATATAAATATACCGATTAATGAGAAAACAGGTCAACATAAAGTA
*
3566556 TCGACAATTGTGCAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGTACGC
130 TCGACAATTGTGCAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACG-GGTGCACGC
3566621 ATAAA
194 ATAAA
*
3566626 GTGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGA-CCCAA-AAACATCGAAACCAATAATTATAATGTAAT
* * * * * *
3566690 ATGTAAATTTACAATGTAACCGATATAAATATATCGGTTTTATGAGAAAATAGGTCAACATAAAG
64 AGGTAAATTAACAATGTAACCGATATAAATATA-CCGATTAATGAGAAAACAGGTCAACATAAAG
* *
3566755 TATCGACACTTGTTG-AATTTGTGTCGATACATT-TTGTCCATAATGAATG-CCAAACGGGTGCA
128 TATCGACAATTG-TGCAATTTGTGTCGATAC-TTATTGTCCAGAATGAATGCCCAAACGGGTGCA
3566817 CGCATAAA
191 CGCATAAA
3566825 GTGTCGATACATTTATTAA
1 GTGTCGATACATTTATTAA
3566844 GGTGGTGTTT
Statistics
Matches: 198, Mismatches: 14, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
199 58 0.29
200 67 0.34
201 69 0.35
202 4 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (198 bp):
GTGTCGATACATTTATTAAAAGTATCGACCCAAAAACATCGAAACCAATAATTATAATGTAATAG
GTAAATTAACAATGTAACCGATATAAATATACCGATTAATGAGAAAACAGGTCAACATAAAGTAT
CGACAATTGTGCAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGGGTGCACGCAT
AAA
Found at i:3567064 original size:31 final size:31
Alignment explanation
Indices: 3567028--3567087 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3567018 AACTTAAAAA
* * *
3567028 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
3567059 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
3567088 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:3567470 original size:20 final size:21
Alignment explanation
Indices: 3567445--3567537 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
3567435 TTTTCCCAAT
*
3567445 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
3567465 TCGCAACT-CGAATTGGGAAAA
1 TCGCAA-TGCGAATTAAGAAAA
*
3567486 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
3567506 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3567527 TCGCAATGCGA
1 TCGCAATGCGA
3567538 TACTGACTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3567490 original size:41 final size:41
Alignment explanation
Indices: 3567445--3567537 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
3567435 TTTTCCCAAT
* *
3567445 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
3567486 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
3567527 TCGCAATGCGA
1 TCGCAATGCGA
3567538 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
Found at i:3567551 original size:20 final size:20
Alignment explanation
Indices: 3567526--3567620 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
3567516 AATTGGGAAA
*
3567526 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * * **
3567546 ATCGCAATGCAATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3567567 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3567587 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3567607 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3567621 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3567836 original size:22 final size:22
Alignment explanation
Indices: 3567808--3567851 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3567798 CACTCTCTCA
3567808 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3567830 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3567852 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3568124 original size:20 final size:20
Alignment explanation
Indices: 3568095--3568138 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3568085 GCGATTTTAG
3568095 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
3568115 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
3568135 TTTC
1 TTTC
3568139 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:3569450 original size:18 final size:18
Alignment explanation
Indices: 3569429--3569473 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3569419 TCCACTTCGG
*
3569429 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3569447 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3569465 GAGCCATCA
1 GAGCCATCA
3569474 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:3570003 original size:19 final size:20
Alignment explanation
Indices: 3569949--3570015 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3569939 TAGTTTACTT
* *
3569949 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3569969 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3569989 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3570008 TCGCAACG
1 TCGCAACG
3570016 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3570023 original size:14 final size:14
Alignment explanation
Indices: 3570004--3570061 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3569994 ATGCGAAATG
3570004 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3570018 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
3570034 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3570050 AAAATCGCAACG
1 AAAATCGCAACG
3570062 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3570046 original size:32 final size:33
Alignment explanation
Indices: 3569988--3570078 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3569978 GGAAATGGCT
3569988 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3570021 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3570053 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3570079 TGCTTTTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3571361 original size:14 final size:14
Alignment explanation
Indices: 3571342--3571377 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3571332 ATTGTTTAAT
3571342 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3571356 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3571370 TGATTTGT
1 TGATTTGT
3571378 TTAATTGATG
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:3571500 original size:20 final size:20
Alignment explanation
Indices: 3571463--3571500 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3571453 GCAAAACAGA
*
3571463 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
3571483 CTATCGCAACGAGGAAAT
1 CTATCGCAACGAGAAAAT
3571501 CGCAATGCGA
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:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:3571521 original size:19 final size:19
Alignment explanation
Indices: 3571497--3571562 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3571487 CGCAACGAGG
3571497 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
3571516 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
3571535 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
3571549 AAATCGCAATGCGA
1 AAATCGCAATGCGA
3571563 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:3571611 original size:20 final size:20
Alignment explanation
Indices: 3571588--3571638 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
3571578 GCGATTTCCT
3571588 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3571608 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3571628 CGTTGCGATAG
1 CGTTGCGATAG
3571639 TCAAATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:3572776 original size:24 final size:24
Alignment explanation
Indices: 3572725--3572778 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3572715 GTATTCGAAA
* *
3572725 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACACAGAC
* *
3572749 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACAGAC
3572773 TTTGAT
1 TTTGAT
3572779 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:3575309 original size:33 final size:33
Alignment explanation
Indices: 3575266--3575431 Score: 219
Period size: 33 Copynumber: 5.0 Consensus size: 33
3575256 CGGAAATTAC
3575266 TATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
**
3575300 -ATCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* **
3575332 TTTCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* * *
3575365 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 TATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
3575399 -ATCGCAATGCGAAATGAAAATCGCAACGTGAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
3575431 T
1 T
3575432 TTAATTTCGC
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
32 3 0.03
33 114 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:3575628 original size:14 final size:14
Alignment explanation
Indices: 3575609--3575645 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3575599 CATCAATTAA
3575609 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3575623 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3575637 ACAAATCAA
1 ACAAATCAA
3575646 TTAAACAATC
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:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3577063 original size:21 final size:21
Alignment explanation
Indices: 3576997--3577063 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3576987 GTGAATCGGG
*
3576997 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3577017 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3577039 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3577060 CTCT
1 CTCT
3577064 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3577082 original size:42 final size:41
Alignment explanation
Indices: 3576997--3577119 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
3576987 GTGAATCGGG
* * * * *
3576997 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
3577039 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
3577081 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
3577120 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:3579191 original size:19 final size:19
Alignment explanation
Indices: 3579105--3579256 Score: 188
Period size: 19 Copynumber: 8.1 Consensus size: 19
3579095 TCTTTTGGTT
*
3579105 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3579124 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3579144 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
3579162 GAAA-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGC
3579178 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
3579198 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3579217 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3579236 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3579255 GA
1 GA
3579257 TTTTGGTTTC
Statistics
Matches: 117, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 5 0.04
18 1 0.01
19 51 0.44
20 45 0.38
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3579212 original size:39 final size:38
Alignment explanation
Indices: 3579105--3579256 Score: 170
Period size: 39 Copynumber: 4.1 Consensus size: 38
3579095 TCTTTTGGTT
* * *
3579105 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATAAAAATCGCAACGC
** *
3579144 GGAAATGACTATCGCAA--CG--A-AAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
3579178 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATAAAAATCGCAACGC
* *
3579217 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
3579255 GA
1 GA
3579257 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
33 14 0.14
34 13 0.13
35 1 0.01
36 2 0.02
38 24 0.25
39 29 0.30
40 14 0.14
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
Found at i:3579268 original size:19 final size:19
Alignment explanation
Indices: 3579246--3579296 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
3579236 GAAATGAAAA
* *
3579246 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGATT
* *
3579265 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTGATT
3579284 TCGCATTGCGATT
1 TCGCATTGCGATT
3579297 ATCTCGTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGATT
Found at i:3579872 original size:20 final size:20
Alignment explanation
Indices: 3579847--3579899 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3579837 GCACTATGTA
3579847 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
3579867 AATCGCGTTGCAAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3579887 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3579900 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3579937 original size:20 final size:20
Alignment explanation
Indices: 3579912--3579961 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3579902 TTGTATTATT
3579912 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
3579932 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
3579952 GCATTGCGAT
1 GCATTGCGAT
3579962 TTTCCCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Found at i:3579980 original size:61 final size:61
Alignment explanation
Indices: 3579848--3579982 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
3579838 CACTATGTAA
* * * * * **
3579848 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTCCATT
* * * * *
3579909 ATTGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTT-CCATT
3579971 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3579983 TTACTTATTC
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
61 56 0.95
62 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCAAAAGTCAGTATCGCATTGCGATTTTCCATT
Found at i:3579999 original size:20 final size:21
Alignment explanation
Indices: 3579950--3580001 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3579940 ATAGTCAGTA
*
3579950 TCGCATTGCGATTTTCCCATT
1 TCGCATTGCGATTTACCCATT
* **
3579971 TCGCGTTGCGATTTACTTA-T
1 TCGCATTGCGATTTACCCATT
3579991 TCGCATTGCGA
1 TCGCATTGCGA
3580002 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTACCCATT
Found at i:3580741 original size:21 final size:21
Alignment explanation
Indices: 3580717--3580773 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
3580707 ATTTTAATAA
3580717 TAAAATAATTATATATAAAAT
1 TAAAATAATTATATATAAAAT
*
3580738 T-AAAT-ATCTATAATATAATAT
1 TAAAATAAT-TAT-ATATAAAAT
*
3580759 TAAAAAAATTA-ATAT
1 TAAAATAATTATATAT
3580774 TTAGTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 2 0.07
20 11 0.37
21 10 0.33
22 5 0.17
23 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATAATTATATATAAAAT
Found at i:3580773 original size:20 final size:20
Alignment explanation
Indices: 3580711--3580773 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
3580701 TATAAAATTT
* *
3580711 TAATAATAAAATAATTATATA
1 TAATATTAAAAAAATTA-ATA
* * **
3580732 TAAAATTAAATATCTATAATA
1 TAATATTAAAAAAAT-TAATA
3580753 TAATATTAAAAAAATTAATA
1 TAATATTAAAAAAATTAATA
3580773 T
1 T
3580774 TTAGTTTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
20 6 0.19
21 23 0.74
22 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATATTAAAAAAATTAATA
Found at i:3580809 original size:36 final size:35
Alignment explanation
Indices: 3580763--3580873 Score: 85
Period size: 36 Copynumber: 3.3 Consensus size: 35
3580753 TAATATTAAA
3580763 AAAATTAATATTTAGTTTATTTTAAAAATTAATATT
1 AAAATTAATATTTA-TTTATTTTAAAAATTAATATT
* * * *
3580799 AAAATTAATATCTA--TAATAT-AATATT-A-A--
1 AAAATTAATATTTATTTATTTTAAAAATTAATATT
* *
3580827 AAAATTAATAT-TTAATTTATTTAAAAAATTAATATT
1 AAAATT-A-ATATTTATTTATTTTAAAAATTAATATT
3580863 AAAATTAATAT
1 AAAATTAATAT
3580874 CTATAATATA
Statistics
Matches: 55, Mismatches: 10, Indels: 21
0.64 0.12 0.24
Matches are distributed among these distances:
28 6 0.11
29 3 0.05
30 3 0.05
31 4 0.07
32 10 0.18
33 5 0.09
34 3 0.05
35 2 0.04
36 19 0.35
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (35 bp):
AAAATTAATATTTATTTATTTTAAAAATTAATATT
Found at i:3580818 original size:65 final size:65
Alignment explanation
Indices: 3580717--3580891 Score: 282
Period size: 64 Copynumber: 2.7 Consensus size: 65
3580707 ATTTTAATAA
*
3580717 TAAAATAATT-ATATATAAAATTAAATATCTATAATATAATATTAAAAAAATTAATATTTAGTTT
1 TAAAA-AATTAATAT-TAAAATT-AATATCTATAATATAATATTAAAAAAATTAATATTTAATTT
3580781 ATT
63 ATT
*
3580784 TTAAAAATTAATATTAAAATTAATATCTATAATATAATATT-AAAAAATTAATATTTAATTTATT
1 TAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATT
*
3580848 TAAAAAATTAATATTAAAATTAATATCTATAATATAAAATTAAA
1 TAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAA
3580892 TATAAAACTT
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
64 61 0.60
65 22 0.22
66 11 0.11
67 8 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (65 bp):
TAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATT
Found at i:3580823 original size:14 final size:12
Alignment explanation
Indices: 3580787--3580873 Score: 79
Period size: 12 Copynumber: 6.9 Consensus size: 12
3580777 GTTTATTTTA
3580787 AAAATTAATATT
1 AAAATTAATATT
3580799 AAAATTAATATCT
1 AAAATTAATAT-T
*
3580812 ATAATATAATATT
1 AAAAT-TAATATT
3580825 AAAAAATTAATATT
1 --AAAATTAATATT
* *
3580839 -TAATTTAT-TT
1 AAAATTAATATT
3580849 AAAAAATTAATATT
1 --AAAATTAATATT
3580863 AAAATTAATAT
1 AAAATTAATAT
3580874 CTATAATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
10 2 0.03
11 6 0.10
12 22 0.36
13 12 0.20
14 15 0.25
15 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:3580842 original size:26 final size:26
Alignment explanation
Indices: 3580789--3580873 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 26
3580779 TTATTTTAAA
3580789 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
3580814 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
3580840 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATTAAAAAATTAATATTAT
3580865 AATTAATAT
1 AATTAATAT
3580874 CTATAATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 16 0.31
25 12 0.23
26 12 0.23
27 1 0.02
28 11 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:3584461 original size:30 final size:30
Alignment explanation
Indices: 3584427--3584499 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3584417 ATTGTGAATC
*
3584427 CTATACCGTGAACTTTGGATTGTTTTACCA
1 CTATACCGTGAACTTTGAATTGTTTTACCA
*
3584457 CTATACCGTGAACTTTGAATTGTTTTACTA
1 CTATACCGTGAACTTTGAATTGTTTTACCA
3584487 CTATACCGTGAAC
1 CTATACCGTGAAC
3584500 GAGTAGGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (30 bp):
CTATACCGTGAACTTTGAATTGTTTTACCA
Done.