Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_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: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:166568 original size:2 final size:2
Alignment explanation
Indices: 166561--166711 Score: 64
Period size: 2 Copynumber: 75.5 Consensus size: 2
166551 AGGGGTTACA
* * *
166561 AT AT AT AT AT AT AT -T AT GT TT AT AT GA- ACT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT
* * * * * *
166603 -T AT GT AT AT AA ACT AT AT AT GT AT AA ACT AT AA AA AGT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* * *
166645 AGT TT AT A- AA AT AT A- AT TT AT AT -T A- AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
166684 AT AT AT AT AT AT AA ACT AT AT AT GT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A
166712 AACTATGCAT
Statistics
Matches: 111, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
1 7 0.06
2 97 0.87
3 7 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:166597 original size:13 final size:13
Alignment explanation
Indices: 166581--166634 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
166571 ATATTATGTT
*
166581 TATATGAACTATA
1 TATATAAACTATA
* *
166594 TATATAAATTATG
1 TATATAAACTATA
166607 TATATAAACTATA
1 TATATAAACTATA
166620 TATGTATAAACTATA
1 TA--TATAAACTATA
166635 AAAAGTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 23 0.68
15 11 0.32
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:166599 original size:15 final size:15
Alignment explanation
Indices: 166590--166717 Score: 87
Period size: 15 Copynumber: 9.1 Consensus size: 15
166580 TTATATGAAC
166590 TATATATATAAA-T-
1 TATATATATAAACTA
*
166603 TATGTATATAAACTA
1 TATATATATAAACTA
*
166618 TATATGTATAAAC--
1 TATATATATAAACTA
*
166631 --TATA-A-AAAGTA
1 TATATATATAAACTA
* *
166642 TATAGTTTATAAAATA
1 TATA-TATATAAACTA
* *
166658 TAATTTATATTAA-TA
1 T-ATATATATAAACTA
*
166673 TATATATATATA-TA
1 TATATATATAAACTA
166687 TATATATATAAACTA
1 TATATATATAAACTA
*
166702 TATATGTATAAACTA
1 TATATATATAAACTA
166717 T
1 T
166718 GCATAACTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
9 3 0.03
10 1 0.01
11 3 0.03
13 13 0.15
14 23 0.26
15 32 0.36
16 12 0.13
17 2 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:166610 original size:26 final size:27
Alignment explanation
Indices: 166562--166622 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
166552 GGGGTTACAA
* *
166562 TATATATATATATTATGTTTATATGAAC
1 TATATATATAAATTATG-TTATATAAAC
166590 TATATATATAAATTATG-TATATAAAC
1 TATATATATAAATTATGTTATATAAAC
166616 TATATAT
1 TATATAT
166623 GTATAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.48
28 16 0.52
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
TATATATATAAATTATGTTATATAAAC
Found at i:166737 original size:17 final size:18
Alignment explanation
Indices: 166715--166751 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
166705 ATGTATAAAC
166715 TATGCATAACTA-ATATA
1 TATGCATAACTACATATA
166732 TATGCATAACTACATATA
1 TATGCATAACTACATATA
166750 TA
1 TA
166752 GTTTATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (18 bp):
TATGCATAACTACATATA
Found at i:166924 original size:14 final size:15
Alignment explanation
Indices: 166907--166945 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
166897 CCTAAACACC
166907 AAACCTTAAATCT-T
1 AAACCTTAAATCTCT
166921 AAACCTTAAA-CTCT
1 AAACCTTAAATCTCT
*
166935 AAACCCTAAAT
1 AAACCTTAAAT
166946 ACTATGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (15 bp):
AAACCTTAAATCTCT
Found at i:167117 original size:22 final size:22
Alignment explanation
Indices: 167092--167194 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
167082 TTTATAAACA
*
167092 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTACTAT
*
167114 ATAGTTTATTCTTAATG-ACCTAT
1 ATAGTTTA-TATTAATGTA-CTAT
* * **
167137 -T-GTATATAATTTATAAAC--T
1 ATAGTTTAT-ATTAATGTACTAT
167156 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTACTAT
167178 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
167195 TAATTATCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.02
20 9 0.14
21 14 0.22
22 29 0.46
23 10 0.16
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (22 bp):
ATAGTTTATATTAATGTACTAT
Found at i:167226 original size:15 final size:15
Alignment explanation
Indices: 167176--167396 Score: 70
Period size: 15 Copynumber: 14.5 Consensus size: 15
167166 TTAATGTACT
*
167176 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
167191 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
167206 ACTATAATTTATATTA
1 A-TATAATTTATATTA
* *
167222 ATATAGTAATATAGTT-
1 ATATAAT-TTATA-TTA
** *
167238 -TATAAACTATA-CA
1 ATATAATTTATATTA
167251 ATATAATTTATA--A
1 ATATAATTTATATTA
*
167264 CATATAGTTTATATTA
1 -ATATAATTTATATTA
*
167280 ATATTAATTTCATA-GA
1 ATA-TAATTT-ATATTA
* *
167296 CTATATTTTATATTA
1 ATATAATTTATATTA
* *
167311 ATATTAATTACAAATT-
1 ATA-TAATT-TATATTA
*
167327 ATAAACTATATTATATTA
1 ATATA--AT-TTATATTA
167345 ATATTAA-TTATATTA
1 ATA-TAATTTATATTA
*
167360 ATATTAA-TTATAAT-
1 ATA-TAATTTATATTA
*
167374 ATATAA-TTATTTTA
1 ATATAATTTATATTA
167388 ATATTAATT
1 ATA-TAATT
167397 ATAAATACTA
Statistics
Matches: 153, Mismatches: 30, Indels: 45
0.67 0.13 0.20
Matches are distributed among these distances:
13 9 0.06
14 33 0.22
15 58 0.38
16 32 0.21
17 16 0.10
18 4 0.03
19 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:167309 original size:31 final size:30
Alignment explanation
Indices: 167250--167319 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
167240 TAAACTATAC
167250 AATA-TAATTTATAACATATAGTTTATATT
1 AATATTAATTTATAACATATAGTTTATATT
*
167279 AATATTAATTTCATAGAC-TATATTTTATATT
1 AATATTAATTT-ATA-ACATATAGTTTATATT
167310 AATATTAATT
1 AATATTAATT
167320 ACAAATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 4 0.11
30 6 0.16
31 25 0.68
32 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (30 bp):
AATATTAATTTATAACATATAGTTTATATT
Found at i:167361 original size:43 final size:43
Alignment explanation
Indices: 167311--167399 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
167301 TTTTATATTA
167311 ATATTAATTACAAATTATAA-ACTAT-ATTATATTAATATTAATT
1 ATATTAA-TACAAATTATAATA-TATAATTATATTAATATTAATT
** *
167354 ATATTAATATTAATTATAATATATAATTATTTTAATATTAATT
1 ATATTAATACAAATTATAATATATAATTATATTAATATTAATT
167397 ATA
1 ATA
167400 AATACTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
42 13 0.32
43 28 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (43 bp):
ATATTAATACAAATTATAATATATAATTATATTAATATTAATT
Found at i:167397 original size:15 final size:15
Alignment explanation
Indices: 167303--167399 Score: 99
Period size: 15 Copynumber: 6.3 Consensus size: 15
167293 AGACTATATT
167303 TTATATTAATATTAA
1 TTATATTAATATTAA
* * *
167318 TTACAAATTATAAACTATA
1 TT--ATATTA-ATATTA-A
167337 TTATATTAATATTAA
1 TTATATTAATATTAA
167352 TTATATTAATATTAA
1 TTATATTAATATTAA
*
167367 TTATAAT-ATA-TAA
1 TTATATTAATATTAA
*
167380 TTATTTTAATATTAA
1 TTATATTAATATTAA
167395 TTATA
1 TTATA
167400 AATACTATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
13 8 0.12
14 6 0.09
15 31 0.47
16 4 0.06
17 10 0.15
18 4 0.06
19 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATTAATATTAA
Found at i:167400 original size:28 final size:27
Alignment explanation
Indices: 167323--167399 Score: 59
Period size: 28 Copynumber: 2.7 Consensus size: 27
167313 ATTAATTACA
*
167323 AATTATAA-ACTATATTATATTAATATT
1 AATTATAATATTA-ATTATATTAATATT
*
167350 AATTATATTAATATTAATTATAATATATAATT
1 AA-T-TA-TAATATTAATTATATTA-AT-ATT
*
167382 -ATTTTAATATTAATTATA
1 AATTATAATATTAATTATA
167400 AATACTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.05
28 15 0.37
29 3 0.07
30 12 0.29
31 6 0.15
32 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTATAATATTAATTATATTAATATT
Found at i:169044 original size:11 final size:11
Alignment explanation
Indices: 169028--169054 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
169018 ATTTTCTTTC
169028 AAGAAATAATG
1 AAGAAATAATG
169039 AAGAAATAATG
1 AAGAAATAATG
169050 AAGAA
1 AAGAA
169055 GGTCGAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (11 bp):
AAGAAATAATG
Found at i:169332 original size:3 final size:3
Alignment explanation
Indices: 169326--169364 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
169316 TTTTTTCATT
169326 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
169365 CTAAATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:170941 original size:14 final size:11
Alignment explanation
Indices: 170929--170962 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
170919 ATATTTTAAA
170929 TAAA-TATTTT
1 TAAATTATTTT
*
170939 TAAATTATATT
1 TAAATTATTTT
170950 TAAATTATTTT
1 TAAATTATTTT
170961 TA
1 TA
170963 GATAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TAAATTATTTT
Found at i:171956 original size:127 final size:127
Alignment explanation
Indices: 171820--172336 Score: 980
Period size: 127 Copynumber: 4.1 Consensus size: 127
171810 ATAATATAAG
*
171820 AAATATAAAGAATATAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
1 AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
*
171885 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATAATAAGTTTATTAT
66 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
171947 AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
1 AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
172012 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
66 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
*
172074 AAATATAAAGAATAAAAAGAATTTGAATTATTACAAAAACAAAATTTATAATATATAAATTATAA
1 AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
*
172139 TTAATATAAAAACTAAATTTCAAAAAATAATCATATTAATTTAATTATCATAAGTTTATTAT
66 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
*
172201 AAATATAAAGAATAAAAAGAATTTGAATTAGTACAAAAACAAAATTTATAATATATAAATTATAA
1 AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
172266 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
66 TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
*
172328 AAATTTAAA
1 AAATATAAA
172337 ATAACATAAT
Statistics
Matches: 383, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 383 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (127 bp):
AAATATAAAGAATAAAAAGAATTTGAATTAATACAAAAACAAAATTTATAATATATAAATTATAA
TTAATATAAAAACTAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAGTTTATTAT
Found at i:173208 original size:21 final size:21
Alignment explanation
Indices: 173192--173245 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
173182 GCGTTGCATT
173192 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
173213 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* *
173234 TCACATTGCGAT
1 TCGCGTTGCGAT
173246 GGTCTACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:173344 original size:20 final size:20
Alignment explanation
Indices: 173316--173450 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
173306 AATTGGGAAA
*
173316 ATCGTAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
173336 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
173356 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
173377 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
173397 TTCACAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
173417 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
173437 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
173451 TTTCAAAGCG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.04
20 63 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:173378 original size:61 final size:61
Alignment explanation
Indices: 173313--173450 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
173303 GCGAATTGGG
* * * * *
173313 AAAATCGTAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
173374 AAAATCGCAACGAGATACTGACTTTCACAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGATAATAC
*
173435 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
173451 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCACAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:173646 original size:22 final size:22
Alignment explanation
Indices: 173618--173661 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
173608 CACTCTCTCA
173618 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
173640 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
173662 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:173969 original size:20 final size:20
Alignment explanation
Indices: 173925--173984 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
173915 ACGATTCTCT
**
173925 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCATTTTCA
*
173945 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCA
* **
173965 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
173985 GAAACTATTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:175322 original size:18 final size:18
Alignment explanation
Indices: 175301--175345 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
175291 TCCACTTCGG
*
175301 GAGCTATCACCTCGCCCA
1 GAGCTATCACCTCACCCA
*
175319 GAGCTATCACCTCACCTA
1 GAGCTATCACCTCACCCA
*
175337 GAGCCATCA
1 GAGCTATCA
175346 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:0.40, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:175881 original size:19 final size:20
Alignment explanation
Indices: 175827--175893 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
175817 TAGTTTACTT
* *
175827 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
175847 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
175867 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
175886 TCGCAACG
1 TCGCAACG
175894 ATAAAATCGC
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:175924 original size:32 final size:33
Alignment explanation
Indices: 175866--175953 Score: 124
Period size: 32 Copynumber: 2.7 Consensus size: 33
175856 GGAAATGGCT
*
175866 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
175899 ATCGCAATGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
** *
175931 ATTACAACGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
175954 TAATGCGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 27 0.56
33 21 0.44
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:175992 original size:14 final size:14
Alignment explanation
Indices: 175973--176030 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
175963 TTGTGTTTCG
175973 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
175987 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
176003 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
176019 CGTTGCGATTTT
1 CGTTGCGATTTT
176031 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:176011 original size:32 final size:33
Alignment explanation
Indices: 175968--176046 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
175958 GCGATTTGTG
*
175968 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
176000 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
176033 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
176047 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:176065 original size:20 final size:19
Alignment explanation
Indices: 176031--176086 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
176021 TTGCGATTTT
*
176031 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
176050 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
176070 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
176087 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:176539 original size:40 final size:41
Alignment explanation
Indices: 176445--176560 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 41
176435 GACTCACCTG
* * *
176445 TCATCCCTCAAGAGTCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
* *
176486 TCCTCCCTCAAGAGTCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
** * * *
176526 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGA-GTCCCTCCCACCGTTCAAGAG
176561 TCCGATTCAC
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 27 0.44
41 22 0.35
42 13 0.21
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:177952 original size:14 final size:14
Alignment explanation
Indices: 177933--177966 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
177923 TGTTTAATTA
177933 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
* *
177947 ATTTGTAAATGTTG
1 ATTTGTAAAAGATG
177961 ATTTGT
1 ATTTGT
177967 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:178127 original size:18 final size:17
Alignment explanation
Indices: 178103--178151 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
178093 TCGCAACGAG
178103 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
178120 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
*
178135 AGGAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
178152 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 10 0.37
15 1 0.04
16 4 0.15
17 1 0.04
18 11 0.41
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:178195 original size:20 final size:20
Alignment explanation
Indices: 178178--178265 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
178168 CGATTTTCTA
178178 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
178198 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
178218 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
178238 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
178258 GTTGCGAT
1 GTTGCGAT
178266 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:178203 original size:34 final size:36
Alignment explanation
Indices: 178158--178245 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
178148 GCGATTTTCA
* *
178158 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
178192 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
178232 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
178246 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:178504 original size:20 final size:20
Alignment explanation
Indices: 178479--178570 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
178469 TTGAAGATGA
178479 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
178499 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
178519 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
178540 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
178560 TTGCGATTTTC
1 TTGCGATTTTC
178571 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:178581 original size:21 final size:21
Alignment explanation
Indices: 178555--178611 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
178545 ATAGTCAGTA
178555 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
178576 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
*
178596 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
178612 AAAGTTTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:179340 original size:24 final size:24
Alignment explanation
Indices: 179313--179366 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
179303 GTATTCGAAA
*
179313 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
179337 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
179361 TTTGAT
1 TTTGAT
179367 GATGTTCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:179556 original size:12 final size:12
Alignment explanation
Indices: 179539--179575 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
179529 CATATAATCT
179539 GAAGAAGAAAAA
1 GAAGAAGAAAAA
179551 GAAGAAGAAAAA
1 GAAGAAGAAAAA
179563 GAAGAAGAAAAA
1 GAAGAAGAAAAA
179575 G
1 G
179576 TCCCGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:181528 original size:12 final size:12
Alignment explanation
Indices: 181513--181556 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
181503 CAAGAAAAAG
181513 GCAATCAAAATT
1 GCAATCAAAATT
* **
181525 GCAATAGAAAAAG
1 GCAAT-CAAAATT
181538 GCAATCAAAATT
1 GCAATCAAAATT
181550 GCAATCA
1 GCAATCA
181557 TCTTTAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (12 bp):
GCAATCAAAATT
Found at i:181534 original size:25 final size:25
Alignment explanation
Indices: 181505--181554 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
181495 TATGGTGTCA
181505 AGAAAAAGGCAATCAAAATTGCAAT
1 AGAAAAAGGCAATCAAAATTGCAAT
181530 AGAAAAAGGCAATCAAAATTGCAAT
1 AGAAAAAGGCAATCAAAATTGCAAT
181555 CATCTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (25 bp):
AGAAAAAGGCAATCAAAATTGCAAT
Found at i:181796 original size:19 final size:19
Alignment explanation
Indices: 181774--181838 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
181764 GGAAATTACT
181774 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
181793 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
181807 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
181826 ATCGCAACGCGAA
1 ATCGCAATGCGAA
181839 TTTAATTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:181797 original size:39 final size:36
Alignment explanation
Indices: 181754--181836 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 36
181744 CTTAATGTCT
*
181754 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
181793 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
181826 ATCGCAACGCG
1 ATCGCAACGCG
181837 AATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
33 26 0.67
35 2 0.05
36 3 0.08
37 1 0.03
39 7 0.18
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:182011 original size:14 final size:14
Alignment explanation
Indices: 181992--182028 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
181982 TATCAATTAA
181992 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
182006 ACAAATCACCTTTT
1 ACAAATCAACTTTT
182020 ACAAATCAA
1 ACAAATCAA
182029 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:183479 original size:80 final size:82
Alignment explanation
Indices: 183365--183533 Score: 267
Period size: 80 Copynumber: 2.1 Consensus size: 82
183355 CCTATTCAAC
183365 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTC-ACGA
183430 TAGGAGTGGACTCTTGAG
65 TAGGAGTGGACTCTTGAG
*
183448 GATG-CAGTGGCCTCTTG-A-GGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCATGAT
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCACGAT
*
183510 AGGAGT-GA-ACTTGAGG
66 AGGAGTGGACTCTTGA-G
183526 GATGACAG
1 GATGACAG
183534 GCGAGTCGGG
Statistics
Matches: 82, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
77 5 0.06
78 7 0.09
79 13 0.16
80 39 0.48
81 1 0.01
82 13 0.16
83 4 0.05
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (82 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCACGAT
AGGAGTGGACTCTTGAG
Found at i:183481 original size:19 final size:19
Alignment explanation
Indices: 183432--183487 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
183422 TTCAACGATA
183432 GGAGTGGACTCTTGAGGAT
1 GGAGTGGACTCTTGAGGAT
* *
183451 GCAGTGGCCTCTTGAGG-T
1 GGAGTGGACTCTTGAGGAT
* *
183469 GGGAGGGGACTCTCGAGGA
1 -GGAGTGGACTCTTGAGGA
183488 ATGATAGGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.21
Consensus pattern (19 bp):
GGAGTGGACTCTTGAGGAT
Found at i:185615 original size:19 final size:19
Alignment explanation
Indices: 185529--185660 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
185519 TCTTTTGGTT
*
185529 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
185548 GATAATGAGCATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
**
185569 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
185586 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
185602 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
185621 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
185640 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
185659 GA
1 GA
185661 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 54 0.56
20 26 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:185689 original size:19 final size:19
Alignment explanation
Indices: 185656--185700 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
185646 AAAATCGCAA
*
185656 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
185675 TGCGATTTTTATTTCGTGT
1 TGCGATTTTGATTTCGCGT
185694 TGCGATT
1 TGCGATT
185701 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:186282 original size:20 final size:20
Alignment explanation
Indices: 186254--186306 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
186244 GCGCTATGTA
186254 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
*
186274 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
186294 TATCTCGTTGCGA
1 AATCACGTTGCGA
186307 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:186344 original size:20 final size:20
Alignment explanation
Indices: 186315--186368 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
186305 GATTTTGTAT
186315 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
186335 TATCGGATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
186355 TATCGCATTGCGAT
1 TATCGCATTGCGAT
186369 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:186401 original size:20 final size:21
Alignment explanation
Indices: 186357--186408 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
186347 ATAGTCAGTA
*
186357 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
186378 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
186398 TCGCATTGCGA
1 TCGCATTGCGA
186409 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:186736 original size:15 final size:17
Alignment explanation
Indices: 186719--186750 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
186709 ACTAAAAAGT
186719 AAAAAA-ATAAATTATA
1 AAAAAACATAAATTATA
186735 AAAAAACATAAATTAT
1 AAAAAACATAAATTAT
186751 TCTGCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAAACATAAATTATA
Found at i:188143 original size:41 final size:42
Alignment explanation
Indices: 188081--188211 Score: 156
Period size: 42 Copynumber: 3.1 Consensus size: 42
188071 CAGATGACCC
188081 GAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGTCA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGTCA
* * * ** *
188123 GAAGGATTT-ATCATCTTGCTCGAAAGACTGACAAATGACCT
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGTCA
* * * * *
188164 GAAGAATTTAATCATCATGCTTGAAAGACTTATTGATGGTCC
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGTCA
188206 GAAGGA
1 GAAGGA
188212 CTTACCAATT
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 34 0.48
42 37 0.52
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (42 bp):
GAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGTCA
Found at i:188191 original size:42 final size:42
Alignment explanation
Indices: 188074--188193 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 42
188064 AGGCTAACAG
* * *
188074 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTA
1 ATGACCAGAAGGATTTAATCATCATGCTCGAAAGACTGACAA
** *
188116 ATGGTCAGAAGGATTT-ATCATCTTGCTCGAAAGACTGACAA
1 ATGACCAGAAGGATTTAATCATCATGCTCGAAAGACTGACAA
* * *
188157 ATGACCTGAAGAATTTAATCATCATGCTTGAAAGACT
1 ATGACCAGAAGGATTTAATCATCATGCTCGAAAGACT
188194 TATTGATGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 34 0.52
42 31 0.48
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGACCAGAAGGATTTAATCATCATGCTCGAAAGACTGACAA
Found at i:190446 original size:12 final size:11
Alignment explanation
Indices: 190429--190548 Score: 98
Period size: 12 Copynumber: 11.5 Consensus size: 11
190419 TGATATGTTC
190429 TCTTTCTTCTCT
1 TCTTTCTTCT-T
190441 TCTTTCTTTCTT
1 TCTTTC-TTCTT
190453 TCTTTCTTTCTT
1 TCTTTC-TTCTT
190465 TCTTTCTTTCTT
1 TCTTTC-TTCTT
190477 TCTTT-TT-TT
1 TCTTTCTTCTT
*
190486 TCTTT-TTTTT
1 TCTTTCTTCTT
190496 TCTTTC-TCTT
1 TCTTTCTTCTT
190506 T-TTTCTTCTT
1 TCTTTCTTCTT
* *
190516 T-TATC-TATT
1 TCTTTCTTCTT
190525 T-TTTCTT-TT
1 TCTTTCTTCTT
*
190534 TCTTT-TTCTA
1 TCTTTCTTCTT
190544 TCTTT
1 TCTTT
190549 TTTTAATATG
Statistics
Matches: 96, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
9 25 0.26
10 31 0.32
12 36 0.38
13 4 0.04
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:190447 original size:4 final size:4
Alignment explanation
Indices: 190429--190516 Score: 103
Period size: 4 Copynumber: 22.2 Consensus size: 4
190419 TGATATGTTC
190429 TCTT TC-T TCTCT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCT-T TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
* *
190477 TCTTT TTTT TCTT T-TT T-TT TCTT TCTCT TTTT TC-T TCTT T
1 TC-TT TCTT TCTT TCTT TCTT TCTT TCT-T TCTT TCTT TCTT T
190517 TATCTATTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
3 12 0.16
4 52 0.70
5 10 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:190547 original size:16 final size:15
Alignment explanation
Indices: 190475--190550 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 15
190465 TCTTTCTTTC
*
190475 TTTCTTTTTTTTCTTT
1 TTTCTTCTTTTTC-TT
* *
190491 TTTTTTCTTTCTCTTT
1 TTTCTTCTTTTTC-TT
190507 TTTCTTCTTTTATCTAT
1 TTTCTTCTTTT-TCT-T
190524 TTT-TTCTTTTTCTT
1 TTTCTTCTTTTTCTT
190538 TTTCTATCTTTTT
1 TTTCT-TCTTTTT
190551 TTAATATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
14 4 0.08
15 4 0.08
16 37 0.73
17 6 0.12
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTCTTTTTCTT
Found at i:196863 original size:2 final size:2
Alignment explanation
Indices: 196858--196893 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
196848 AAAATAGATA
196858 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
196894 TCATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205674 original size:19 final size:20
Alignment explanation
Indices: 205661--205697 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
205651 AAAATTGAAA
205661 AGATT-TAATAAAATAAAAT
1 AGATTATAATAAAATAAAAT
205680 AGATTATAAT-AAATAAAA
1 AGATTATAATAAAATAAAA
205698 GGGAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AGATTATAATAAAATAAAAT
Found at i:205739 original size:27 final size:27
Alignment explanation
Indices: 205685--205739 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
205675 AAAATAGATT
*
205685 ATAATAAATAAAAGGGAAAATAATAAA
1 ATAATAAATAAAAGAGAAAATAATAAA
* *
205712 ATAATAAATAATAGTAGTAAATAA-AAA
1 ATAATAAATAAAAG-AGAAAATAATAAA
205739 A
1 A
205740 GGGTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (27 bp):
ATAATAAATAAAAGAGAAAATAATAAA
Found at i:205798 original size:17 final size:18
Alignment explanation
Indices: 205762--205803 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
205752 GTTGTTTTTA
205762 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
205780 AAATAAAATA-AATAATT
1 AAATAAAAGATAAGAATT
205797 AAATAAA
1 AAATAAA
205804 TAATTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:208529 original size:21 final size:21
Alignment explanation
Indices: 208490--208528 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
208480 GTTTGCTAAA
208490 AAATAAAATAAAAATAAAACG
1 AAATAAAATAAAAATAAAACG
*
208511 AAATACAAT-AAAATAAAA
1 AAATAAAATAAAAATAAAA
208529 AATAGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAACG
Found at i:219139 original size:21 final size:21
Alignment explanation
Indices: 219115--219157 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
219105 TTACCAGAAT
219115 ACCTATGAGGCATCTAGTAAA
1 ACCTATGAGGCATCTAGTAAA
219136 ACCTATGAGGCATCTAGTAAA
1 ACCTATGAGGCATCTAGTAAA
219157 A
1 A
219158 GTTTAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (21 bp):
ACCTATGAGGCATCTAGTAAA
Found at i:224092 original size:51 final size:51
Alignment explanation
Indices: 223996--224106 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 51
223986 AACTAATGAG
* *
223996 TAAAATAATAATAAATGAAAGATAATGTTTTGATTATATTCTAATTCCA-AA
1 TAAAATAATAATAAATGAAAGATAATGTTTTAAATATATTCTAATT-CATAA
*
224047 TAAAATAATAATAAACT-AAA-ACTAATGTTTTAAATCTA-TCTTAATTCATAA
1 TAAAATAATAATAAA-TGAAAGA-TAATGTTTTAAATATATTC-TAATTCATAA
224098 TAAAA-AATA
1 TAAAATAATA
224107 TATATCTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
50 9 0.17
51 43 0.81
52 1 0.02
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (51 bp):
TAAAATAATAATAAATGAAAGATAATGTTTTAAATATATTCTAATTCATAA
Found at i:235275 original size:2 final size:2
Alignment explanation
Indices: 235268--235333 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
235258 ACTGGATTTA
235268 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
235310 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
235334 GACTTTAGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238058 original size:54 final size:54
Alignment explanation
Indices: 237974--238929 Score: 1096
Period size: 54 Copynumber: 17.8 Consensus size: 54
237964 AAGGTTCTCT
* * *
237974 ATCAACATATGATGTATTCCATACTGTGCACACTTAGTGCCGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* *
238028 ATCAATATATGATGAATTCCGTACTTTGCACACTTAGTGCTGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* *
238082 ATTAACATATGATGAATTTCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* ** * ** * *
238136 ATCAACAAATGATGAATTCTATACTTTTCATGCTTACTGTCGAAACGGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* **
238190 ATCAACATATGATGAATTCCGTACTTTGCACGCTTAGTGCCGAAATAGTT-TTCC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATT-C
* * * * ***
238244 ATCAATATATGATGAATT-TGTACTTT-TACACTTAGTGTCGAAA-TAATATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * * * *
238295 ATCAACATATGATGAATTTCATACTTTGCACACCTAGTGTCGAAACAGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * **
238349 ATCAACATATAATGAATGT-CTTACTTTGCACACTTAGTGCCGAAATAGTTATTC
1 ATCAACATATGATGAAT-TCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* ** *
238403 ATTAACATATGATGAATTATGTACTTTGCACACTTAGTGCCGAAACGGTTTTTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * * * * * *
238457 ATCAACATATGATGAATTTCGTACATTGCACAATTAGTGTCGTAATGGTTATTT
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
** * * *
238511 A-CTAACATATGATGAATTATGTACTTTGCACACTTAGAGTCGAAACGGTTTTTC
1 ATC-AACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
** ** *
238565 ATCATTATATGATGAATTATGTACTTTGCACACTTAGTGCCGAAACAGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * * * ** **
238619 ATTAACATATGATGAATTCCATAGTTTTCACACTTAGTATCGAAACAATTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
** * ** * *
238673 ATCAACATATGATGAATTATGTACTTTGTACACTTAGTATCGAAACGATTATTG
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * *
238727 ATCAACATATGATGAATTCCGTACTTTGTACACTTAGTACCGAAATGGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* *
238781 ATCAACATATGATGAATTTCGTACTTTGCACACTTAGTGCCGAAACGATTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
** * * *
238835 ATCAACATATGATGAATTATGTACTTTGCAAACTTAGTGTCGAAACAGTTATTC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
* * *
238889 ATCAACATATAATGAGTTTCGTACTTTGCACACTTAGTGCC
1 ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCC
238930 TATTTGGTAA
Statistics
Matches: 769, Mismatches: 124, Indels: 18
0.84 0.14 0.02
Matches are distributed among these distances:
51 19 0.02
52 22 0.03
53 26 0.03
54 700 0.91
55 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (54 bp):
ATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGGTTATTC
Found at i:238980 original size:18 final size:18
Alignment explanation
Indices: 238957--238991 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
238947 ACACATAATA
238957 ATTAATCAT-ACATATATG
1 ATTAAT-ATAACATATATG
238975 ATTAATATAACATATAT
1 ATTAATATAACATATAT
238992 TTTCACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAATATAACATATATG
Found at i:240822 original size:54 final size:54
Alignment explanation
Indices: 240742--243133 Score: 2962
Period size: 54 Copynumber: 44.3 Consensus size: 54
240732 ATTCCATGGG
* * * * *
240742 TTGCACACATAGTTCCAAAACGGTTATTCATCAACATATGATAAATTTCGTTCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * * *
240796 TTGCACATTTACTCCCGAAACAGTTATTCACCAACATATGATGAATTAT-GTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTACT
* * * *
240850 TT-CATAGTTAATGCCGAAACGGTTATTCATCAACATATGATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* ** * * * *
240903 TTGCACACTTACTTTCGGAATGATTATTCATCAATATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
** * * *
240957 TTGCACACTTAGTGTTGAAACGGTTATTCATCCACATATGATGAATTTCATACG
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
241011 TTGCACGCTTAGTGTCGAAGCGGTTATTCATCAACATATGATGAATTTCATACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
241065 TTGCACGCTTAGTGTCGAAACGATTATTCATCAACATATGATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
** ** * * *
241119 TTGCACACTTTGAGTGTTGAAACTATTATTCATTAGCATATGATGAATTCCGTACT
1 TTGCACAC-TT-AGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
** * *
241175 TTGTTCGCTTAGTGCCGAAACGGTTATTCATCAACATATGATGAA-TTCGTTACC
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCG-TACT
* **
241229 TTGCACACTTAGTGTCGAAATTGTTATTCATCAACATATGATGAATTAT-GTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTACT
* * * *
241283 TTGCACACTTAGTGCCGAAATGGTTTTTCATCAACATATGATGAATTCCATACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
241337 TTCCATACTTAGTGCCGAAATGATTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * ** * **
241391 TTACACACTTAGTACTAAAACGGTTATTCATCAATATATGATGAATACCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * * * *
241445 TTTCACGCTTAGTGTCGAAACGATTATTCATCAACATAAGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * *
241499 TTACACGCTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTAGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
241553 TTGCACACTTAATGTCGAAACGGTTATTCATCAACATATGTTGAATTTCATACAT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTAC-T
* *
241608 TT-CACGA-TTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTAT-TTACT
1 TTGCAC-ACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTACT
* * * ** * *
241661 TTGCACCCTTTGTG-CTACAACAATTTTTCATCAATATATGATGAA-TTCTGTACT
1 TTGCACACTTAGTGCCGA-AACGGTTATTCATCAACATATGATGAATTTC-GTACT
* * * * * *
241715 TTGAACACTTAGTGTCGTAACGGTTATTTAACAATATATGATGAA-TTCTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTC-GTACT
* * * * *
241769 TTGCACACCTAGTGCTGAAACGGTTATTCATCAATATATTAAGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * *
241823 TTGCACACTTAGTGCTGAAATGGTTATTCATCAACATATGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * * *
241877 TTGAACACCTAGTGCCGAAACAGTTATTCATCAACATATGATAAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* *
241931 TTGCACACTTAGTACCGAAATGGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* *
241985 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATAAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
*
242039 TTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
*
242093 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* ** * *
242147 TTGCACACTTTGTGCCGAAATAGTTATTCATCAACATATAAAGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * *
242201 TTACACACTTAGTGCCGAAACAGTTATACATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * ** *
242255 TTGCACACTTAGTTCCAAAATGGTTATTCATCAACATATGATGAACATAGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * * * *
242309 TTTCACGCTTAGTGTCGAAACTGTTATTCATCAACATATGATGAAGTTCGTAGT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
242363 TTGCACGCTTAGTGCCGAAACGGTTTTTTTATCAACATATGATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGG-TTATTCATCAACATATGATGAATTTCGTACT
* * *
242418 TTGCACACTTAGTGTCGAAACGG-TATTCATCAACATATGATGAATTCCATACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
*
242471 TTGCACACTTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * *
242525 TTGCACACCTAGTGCCCAAACGGCTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
*
242579 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* *
242633 TTGCACACTTAGTGCCGAAACGGTTTTTCATCAACATATGATGAATTACGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * * * *
242687 TTGCACACTTAGTGCAGAAATGATTATTCATTAACATATGATGAATTTTGTAAT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * *
242741 TTGCACATTTAGTGTCGAAACGGTTTTTCATCAACATATGATGAATAATT--TACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAAT--TTCGTACT
* * * *
242795 TTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCCTTAGT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* ** *
242849 TTTCACACTTAGTATCG-AACGGTTATTCATCAACATATGATGAATTAT-GTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTACT
*
242902 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
** *
242956 TTGCACACTTAGTGTTGAAATGGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
* * * *
243010 TTGCACACTTAGTTCTGAAATGGTTATTCATCACCATATGATGAATTAT-GTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTACT
* * * * *
243064 TTGCACACTAAGTGTCGAAACGGTTAATCATCAAAATATGATGAATTTCGTATT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
243118 TTGCACACTTAGTGCC
1 TTGCACACTTAGTGCC
243134 TATTTGGTAA
Statistics
Matches: 2024, Mismatches: 284, Indels: 60
0.85 0.12 0.03
Matches are distributed among these distances:
52 3 0.00
53 147 0.07
54 1764 0.87
55 64 0.03
56 46 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (54 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACT
Found at i:247544 original size:104 final size:104
Alignment explanation
Indices: 247356--247545 Score: 317
Period size: 104 Copynumber: 1.8 Consensus size: 104
247346 CTTTAAATTA
* * *
247356 TCCAGATTGACCTGATTTCCTCAACGAGAAGGAACAACGTCATATGAAAGCGGCCAGAACTCTTC
1 TCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
*
247421 AATATGGATGAGCAGTGTCATACTCAATAATATATTTTC
66 AATATGGATGAGCAATGTCATACTCAATAATATATTTTC
* *
247460 TCCATATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
1 TCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
*
247525 AATATGGATGAGTAATGTCAT
66 AATATGGATGAGCAATGTCAT
247546 CTTCAACGCC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 79 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (104 bp):
TCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
AATATGGATGAGCAATGTCATACTCAATAATATATTTTC
Found at i:247560 original size:104 final size:104
Alignment explanation
Indices: 247356--247593 Score: 307
Period size: 104 Copynumber: 2.3 Consensus size: 104
247346 CTTTAAATTA
* * * *
247356 TCCAGATTGACCTGATTTCCTCAACGAGAAGGAACAACGTCATATGAAAGCGGCCAGAACTCTTC
1 TCCAGATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
* * * *
247421 AATATGGATGAGCAGTGTCATACTCAATAATATATTTTC
66 AATATGGATGAGCAATGTCATACTCAACAACATATTATC
*
247460 TCCATATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
1 TCCAGATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
* **
247525 AATATGGATGAGTAATGTCAT-CTTCAACGCCATATTATC
66 AATATGGATGAGCAATGTCATAC-TCAACAACATATTATC
** * * *
247564 TCTGGATTGACTCAACTTCCTCAATGAGAA
1 TCCAGATTGACCCGATTTCCTCAATGAGAA
247594 TGAATAGTGT
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
103 1 0.01
104 114 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (104 bp):
TCCAGATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGGCCAAAACTCTTC
AATATGGATGAGCAATGTCATACTCAACAACATATTATC
Found at i:247795 original size:3 final size:3
Alignment explanation
Indices: 247787--247815 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
247777 TGCCTAATGT
247787 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
247816 TTAATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:248805 original size:2 final size:2
Alignment explanation
Indices: 248798--248827 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
248788 TTATTTCTGA
248798 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
248828 TGTTAGTCAT
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:248999 original size:2 final size:2
Alignment explanation
Indices: 248994--249026 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
248984 TATGCGTGTG
248994 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
249027 GCCTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:250205 original size:83 final size:83
Alignment explanation
Indices: 250118--250301 Score: 206
Period size: 83 Copynumber: 2.2 Consensus size: 83
250108 CAACATGGTT
* *
250118 GTTTATAGTGGCGTTTATCCAACAAACGACACTATAGAATAGTAATTTAGCGGCGTTTATCAAAC
1 GTTTATAGTGGCGTTTATCCAACAAACGACACTATAGAATAGTAATGTAGCAGCGTTTATCAAAC
*
250183 AAACACCGCAATAGTGTC
66 AAACACCGAAATAGTGTC
* * * * * * * * * **
250201 GTTTAAAGTGGCGTTTGTGCAACAAATGCCGCTATAGAGTAGTAATGTAGCAGCTTTTTTCCTAC
1 GTTTATAGTGGCGTTTATCCAACAAACGACACTATAGAATAGTAATGTAGCAGCGTTTATCAAAC
* * *
250266 AAACGCCGAAATATTGTT
66 AAACACCGAAATAGTGTC
*
250284 GTTTATAATGGCGTTTAT
1 GTTTATAGTGGCGTTTAT
250302 TATAAAAACT
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (83 bp):
GTTTATAGTGGCGTTTATCCAACAAACGACACTATAGAATAGTAATGTAGCAGCGTTTATCAAAC
AAACACCGAAATAGTGTC
Found at i:250751 original size:22 final size:22
Alignment explanation
Indices: 250721--250762 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
250711 GTTTTTCTAC
*
250721 TTTCGAATAGAAAAATAATATT
1 TTTCAAATAGAAAAATAATATT
*
250743 TTTCAAATAGGAAAATAATA
1 TTTCAAATAGAAAAATAATA
250763 GCTTTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (22 bp):
TTTCAAATAGAAAAATAATATT
Found at i:251943 original size:42 final size:42
Alignment explanation
Indices: 251819--252052 Score: 180
Period size: 42 Copynumber: 5.6 Consensus size: 42
251809 CATTTATAGC
*
251819 GGCGCTTTTTAATCAAACGCCGCAAAATACTCT-TAATTTAGT
1 GGCGTTTTTTAATCAAACGCCGCAAAATACT-TGTAATTTAGT
* * * * *
251861 GGCGTTTATT-ACCAAACACCGTTAAAA-ACTTGTACTTTAGT
1 GGCGTTTTTTAATCAAACGCCG-CAAAATACTTGTAATTTAGT
251902 GGCGTTTTTTAATCAAACGCCGCAAAATACTCT-TAATTTAGT
1 GGCGTTTTTTAATCAAACGCCGCAAAATACT-TGTAATTTAGT
* * * * *
251944 GTCGTTTATT-ACCAAGACGACGCTAAAA-ACTTGTACTTTAGT
1 GGCGTTTTTTAATCAA-ACGCCGC-AAAATACTTGTAATTTAGT
* * * * *
251986 AGCGTTTTTGACAT-AAACACCGCAATAAT-TTTGTAAGTTAGT
1 GGCGTTTTTTA-ATCAAACGCCGCAA-AATACTTGTAATTTAGT
*
252028 GGTGTTTTTGTAAT-AAACGCCGCAA
1 GGCGTTTTT-TAATCAAACGCCGCAA
252053 TAGTTTTGTC
Statistics
Matches: 149, Mismatches: 30, Indels: 26
0.73 0.15 0.13
Matches are distributed among these distances:
40 1 0.01
41 40 0.27
42 99 0.66
43 8 0.05
44 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (42 bp):
GGCGTTTTTTAATCAAACGCCGCAAAATACTTGTAATTTAGT
Found at i:251994 original size:83 final size:83
Alignment explanation
Indices: 251824--251994 Score: 290
Period size: 83 Copynumber: 2.0 Consensus size: 83
251814 ATAGCGGCGC
*
251824 TTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGGCGTTTATTACCAAACACCGTTAAAAA
1 TTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGGCGTTTATTACCAAACACCGCTAAAAA
*
251889 CTTGTACTTTAGTGGCGT
66 CTTGTACTTTAGTAGCGT
*
251907 TTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGTCGTTTATTACCAAGACGA-CGCTAAA
1 TTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGGCGTTTATTACCAA-AC-ACCGCTAAA
251971 AACTTGTACTTTAGTAGCGT
64 AACTTGTACTTTAGTAGCGT
251991 TTTT
1 TTTT
251995 GACATAAACA
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
83 51 0.61
84 31 0.37
85 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (83 bp):
TTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGGCGTTTATTACCAAACACCGCTAAAAA
CTTGTACTTTAGTAGCGT
Found at i:252027 original size:84 final size:82
Alignment explanation
Indices: 251824--252034 Score: 241
Period size: 84 Copynumber: 2.5 Consensus size: 82
251814 ATAGCGGCGC
* * *
251824 TTTTT-AATCAAACGCCGCAAAATACTCTTAATTTAGTGGCGTTTATTACCAAACACCGTTAAAA
1 TTTTTGAATCAAACACCGCAAAATA-TCTTAAGTTAGTGGCGTTTATTACCAAACACCGCTAAAA
*
251888 ACTTGTACTTTAGTGGCG
65 ACTTGTACTTTAGTAGCG
* * * *
251906 TTTTTTAATCAAACGCCGCAAAATACTCTTAATTTAGTGTCGTTTATTACCAAGACGA-CGCTAA
1 TTTTTGAATCAAACACCGCAAAATA-TCTTAAGTTAGTGGCGTTTATTACCAA-AC-ACCGCTAA
251970 AAACTTGTACTTTAGTAGCG
63 AAACTTGTACTTTAGTAGCG
* *
251990 TTTTTGACAT-AAACACCGCAATAAT-TTTGTAAGTTAGTGGTGTTT
1 TTTTTGA-ATCAAACACCGCAA-AATATCT-TAAGTTAGTGGCGTTT
252035 TTGTAATAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
82 5 0.04
83 48 0.42
84 55 0.48
85 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (82 bp):
TTTTTGAATCAAACACCGCAAAATATCTTAAGTTAGTGGCGTTTATTACCAAACACCGCTAAAAA
CTTGTACTTTAGTAGCG
Found at i:252118 original size:42 final size:42
Alignment explanation
Indices: 251998--252119 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
251988 CGTTTTTGAC
* *** ** *
251998 ATAAACACCGCAATAATTTTGTAAGTTAGTGGTGTTTTTGTA
1 ATAAACACCGCAATAGTTTTGTCCCTTAGTGGCATTTTCGTA
* * *
252040 ATAAACGCCGCAATAGTTTTGTCCCTTAGAGACATTTTCGTA
1 ATAAACACCGCAATAGTTTTGTCCCTTAGTGGCATTTTCGTA
*
252082 ATAAACACCGCAATAGTTTTGTCCCTTTGTGGCATTTT
1 ATAAACACCGCAATAGTTTTGTCCCTTAGTGGCATTTT
252120 TAATATAAAC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (42 bp):
ATAAACACCGCAATAGTTTTGTCCCTTAGTGGCATTTTCGTA
Found at i:260631 original size:44 final size:43
Alignment explanation
Indices: 260578--260756 Score: 150
Period size: 44 Copynumber: 4.1 Consensus size: 43
260568 TTTGTAACAG
* * *
260578 AAAACGCCGCTATATACCATACCTTTTGTGATGTTTGTATCCTA
1 AAAACGCCGCTATATACCAGACCTTTTGTGATGTTTATAT-CGA
* * * *
260622 AAAATGCCGCTATATACCAGACCTGTTGCGGTGTTTATAT-GA
1 AAAACGCCGCTATATACCAGACCTTTTGTGATGTTTATATCGA
* *
260664 AAAACGCCGCTATATA-TA-ACACTTTTAG-CAGTGTTTATATCCGA
1 AAAACGCCGCTATATACCAGAC-CTTTT-GTGA-TGTTTATAT-CGA
* * ** * *
260708 CAAACGCCACTATATACCAGACCTTTTGTGGCGTTTGTATCTA
1 AAAACGCCGCTATATACCAGACCTTTTGTGATGTTTATATCGA
260751 AAAACG
1 AAAACG
260757 TCGAAATATC
Statistics
Matches: 106, Mismatches: 21, Indels: 17
0.74 0.15 0.12
Matches are distributed among these distances:
40 2 0.02
41 5 0.05
42 26 0.25
43 7 0.07
44 58 0.55
45 6 0.06
46 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (43 bp):
AAAACGCCGCTATATACCAGACCTTTTGTGATGTTTATATCGA
Found at i:265574 original size:20 final size:19
Alignment explanation
Indices: 265546--265607 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
265536 ATTAAGCTAC
265546 GAATCTGAAAGTAAAGTTAT
1 GAATCTGAAAGTAAA-TTAT
*
265566 GAATATGAAAGTAAATGTAT
1 GAATCTGAAAGTAAAT-TAT
*
265586 TAATCTGAAA-TAAATTAT
1 GAATCTGAAAGTAAATTAT
265604 GAAT
1 GAAT
265608 TTGGAATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.16
19 6 0.16
20 25 0.68
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.32
Consensus pattern (19 bp):
GAATCTGAAAGTAAATTAT
Found at i:271596 original size:3 final size:3
Alignment explanation
Indices: 271588--271641 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
271578 GGGTTTGTAG
271588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
271635 -AT AAT AA
1 AAT AAT AA
271642 CGAAAATGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:272028 original size:80 final size:80
Alignment explanation
Indices: 271863--272046 Score: 192
Period size: 80 Copynumber: 2.3 Consensus size: 80
271853 GAATTGAGTG
271863 AAGGTTGAGCAAGTTCTTCTCATTAAAAGCTTCTTCTATTGGCAATGCTGATCCAACTCCTTCTG
1 AAGGTTGAGCAAGTTCTTCTCATTAAAAGCTTCTTCTATTGGCAATGCTGATCCAACTCCTTCTG
** *
271928 TGATAGATTCGAGCA
66 TGATAGAAACGACCA
* * * * * * * * *
271943 GAGGTTGAGCAAGTTCTTCTCGTTACGAA-TTTTTTCTCTTATG-AATGCTGATCTAACTCTTTC
1 AAGGTTGAGCAAGTTCTTCTCATTA-AAAGCTTCTTCTATT-GGCAATGCTGATCCAACTCCTTC
*
272006 TGTGATGGAAACGACCA
64 TGTGATAGAAACGACCA
* * *
272023 AAGGTTGAGTAAGTTATTATCATT
1 AAGGTTGAGCAAGTTCTTCTCATT
272047 CTAAACTTCT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
80 81 0.96
81 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (80 bp):
AAGGTTGAGCAAGTTCTTCTCATTAAAAGCTTCTTCTATTGGCAATGCTGATCCAACTCCTTCTG
TGATAGAAACGACCA
Found at i:276067 original size:32 final size:33
Alignment explanation
Indices: 275990--276071 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
275980 AGTGACTTTT
* *
275990 TGCCTCAAAGAAAGGT-GAAAGTATGAATTTGGG
1 TGCCTCAAAGAGAGGTAG-TAGTATGAATTTGGG
*
276023 TGCCTTAAAGAGAGGTAGTAGTATGAATTT-GG
1 TGCCTCAAAGAGAGGTAGTAGTATGAATTTGGG
*
276055 TGCCTCAGAGAGAGGTA
1 TGCCTCAAAGAGAGGTA
276072 ATGTCAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 17 0.40
33 25 0.58
34 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.26
Consensus pattern (33 bp):
TGCCTCAAAGAGAGGTAGTAGTATGAATTTGGG
Found at i:276485 original size:25 final size:25
Alignment explanation
Indices: 276439--276486 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
276429 TCGCTTCATA
*
276439 ATGTCCCATAATTCATCGAATGTCC
1 ATGTCCCATAATTCATCAAATGTCC
276464 ATGTCCCATAA-TCGATCAAATGT
1 ATGTCCCATAATTC-ATCAAATGT
276487 TGAATCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (25 bp):
ATGTCCCATAATTCATCAAATGTCC
Found at i:287113 original size:34 final size:33
Alignment explanation
Indices: 287075--287146 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 33
287065 TACAACAAAG
287075 TTACAATAA-GTATTAAATGGTAAATAATAAAAAA
1 TTACAATAATGTATTAAATGGT-AATAA-AAAAAA
*
287109 TTACAATAACTTGTATTAAATGGTAATAAACAAAA
1 TTACAATAA--TGTATTAAATGGTAATAAAAAAAA
287144 TTA
1 TTA
287147 ATTAACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
34 9 0.26
35 8 0.24
36 5 0.15
37 12 0.35
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (33 bp):
TTACAATAATGTATTAAATGGTAATAAAAAAAA
Found at i:287391 original size:15 final size:15
Alignment explanation
Indices: 287373--287419 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
287363 GTCATCACCA
*
287373 TCATCATCATAGTCG
1 TCATCATCATCGTCG
* *
287388 TCATCATCGTCGTTG
1 TCATCATCATCGTCG
*
287403 TCATCGTCATCGTCG
1 TCATCATCATCGTCG
287418 TC
1 TC
287420 GTTGTCAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (15 bp):
TCATCATCATCGTCG
Found at i:287409 original size:21 final size:21
Alignment explanation
Indices: 287385--287426 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
287375 ATCATCATAG
287385 TCGTCATCATCGTCGTTGTCA
1 TCGTCATCATCGTCGTTGTCA
*
287406 TCGTCATCGTCGTCGTTGTCA
1 TCGTCATCATCGTCGTTGTCA
287427 GGAGAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGTCATCATCGTCGTTGTCA
Found at i:288396 original size:62 final size:64
Alignment explanation
Indices: 288330--288457 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 64
288320 AAAATAATAT
*
288330 TTAATATG-A-ATATATATATATTATACAAAAGGTAAAAATATGTAAAGTATGGCATGTAACCC
1 TTAATATGAATATATATATATATTATACAAAAGGTAAAAATATGTAAAGTACGGCATGTAACCC
*
288392 TTAATATGAATATATATATATATATTATACAAAAGGTAAAAATATGTAAAGTACGTCATGTAACC
1 TTAATATG-A-ATATATATATATATTATACAAAAGGTAAAAATATGTAAAGTACGGCATGTAACC
288457 C
64 C
288458 CTAGGCACGA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
62 8 0.13
65 1 0.02
66 51 0.85
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (64 bp):
TTAATATGAATATATATATATATTATACAAAAGGTAAAAATATGTAAAGTACGGCATGTAACCC
Found at i:302231 original size:13 final size:13
Alignment explanation
Indices: 302213--302247 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
302203 TTTAAGATTT
302213 TTTTTGAAAATCA
1 TTTTTGAAAATCA
302226 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
302238 ATTTTGAAAA
1 TTTTTGAAAA
302248 ATTACTCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:303817 original size:12 final size:12
Alignment explanation
Indices: 303799--303823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
303789 AGGTGGAATA
303799 GGAGGTTGGTTT
1 GGAGGTTGGTTT
303811 GGAGGTTGGTTT
1 GGAGGTTGGTTT
303823 G
1 G
303824 ACCGACTAGA
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:0.08, C:0.00, G:0.52, T:0.40
Consensus pattern (12 bp):
GGAGGTTGGTTT
Found at i:313603 original size:54 final size:54
Alignment explanation
Indices: 313545--313647 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
313535 CAAAATGGAA
** *
313545 ATTCACAAACGTATTACGAATTCCATGGATTGCACACATAGTGCCGAAATGGTC
1 ATTCACAAACACATTACGAATACCATGGATTGCACACATAGTGCCGAAATGGTC
* * * **
313599 ATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTGCCGAAA
1 ATTCACAAACACATTACGAATACCATGGATTGCACACATAGTGCCGAAA
313648 ATGCACTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
ATTCACAAACACATTACGAATACCATGGATTGCACACATAGTGCCGAAATGGTC
Found at i:328476 original size:17 final size:16
Alignment explanation
Indices: 328458--328503 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
328448 GAAAAAAAGA
328458 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
*
328474 -AAAAATTGAAAAAAATG
1 AAAAAAATG--AAAAATG
328491 AAAAAAATGAAAA
1 AAAAAAATGAAAA
328504 GAAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 4 0.16
17 7 0.28
18 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:328477 original size:24 final size:24
Alignment explanation
Indices: 328446--328495 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
328436 TTGCTTGAAG
*
328446 ATGAAAAAAAGAAAAAAAATGAAAA
1 ATGAAAAATAG-AAAAAAATGAAAA
*
328471 ATGAAAAATTGAAAAAAATGAAAA
1 ATGAAAAATAGAAAAAAATGAAAA
328495 A
1 A
328496 AATGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (24 bp):
ATGAAAAATAGAAAAAAATGAAAA
Found at i:328487 original size:10 final size:9
Alignment explanation
Indices: 328446--328503 Score: 70
Period size: 9 Copynumber: 6.8 Consensus size: 9
328436 TTGCTTGAAG
328446 ATGAAAAAA
1 ATGAAAAAA
328455 A-GAAAAAAA
1 ATG-AAAAAA
328464 ATG--AAAA
1 ATGAAAAAA
328471 ATG-AAAAA
1 ATGAAAAAA
*
328479 TTGAAAAAA
1 ATGAAAAAA
328488 ATGAAAAAA
1 ATGAAAAAA
328497 ATGAAAA
1 ATGAAAA
328504 GAAAAACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 7 0.16
8 7 0.16
9 28 0.65
10 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:329965 original size:54 final size:53
Alignment explanation
Indices: 329852--331004 Score: 1741
Period size: 53 Copynumber: 21.7 Consensus size: 53
329842 GCAACAGAAG
* *
329852 ATTGTTCGAGTTCTACTCCCTGAAGAAATA-TG-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
329903 ATTTTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
329957 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
330010 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAG-AGAGCCTGTAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
330064 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330117 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
330171 ATTGTTCGAGCTCTACTCCCTGAAGAAATAG-G-GTGGACCCGGAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330222 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330276 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGAAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330329 ATTGTTCGAGTTTTACTCCCTGAAGAAATAGAGAGCGGACCAGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330382 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330436 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330489 ATTGTTCGAGTTCTTACTCCTTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330543 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCTGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330596 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330649 ATTATTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330703 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCATAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330754 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCATAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
330808 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330861 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCTCGTAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* * *
330915 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGATAGCAGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330969 ATTGTTGGAGTTCTACTCCCTGAAGAAATAGGGAGC
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC
331005 AAATACGATT
Statistics
Matches: 1015, Mismatches: 64, Indels: 44
0.90 0.06 0.04
Matches are distributed among these distances:
51 72 0.07
52 54 0.05
53 454 0.45
54 433 0.43
55 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:330036 original size:107 final size:107
Alignment explanation
Indices: 329852--331004 Score: 1812
Period size: 107 Copynumber: 10.8 Consensus size: 107
329842 GCAACAGAAG
* * * *
329852 ATTGTTCGAGTTCTACTCCCTGAAGAAATA-TG-GTGGACCCGTAGGAAGATTATTTTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
329915 CTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAAT
66 CTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
329957 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* * *
330022 CTTACTCCCTGAAGAAATAGAGAG-AGAGCCTGTAGGAAGAAT
66 CTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
330064 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* *
330129 CTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * * *
330171 ATTGTTCGAGCTCTACTCCCTGAAGAAATAG-G-GTGGACCCGGAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* *
330234 CTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330276 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGAAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
330341 -TTACTCCCTGAAGAAATAGAGAGCGGACCAGTAGGAAGATT
66 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
330382 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
330447 TC-TACTCCCTGAAGAAATAGAGAGCGGACTCGTAGGAAGATT
65 TCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
330489 ATTGTTCGAGTTCTTACTCCTTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTTGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
330554 TC-TACTCCCTGAAGAAATAGAGAGCGGACCTGTAGGAAGATT
65 TCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330596 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
330661 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
330703 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCATAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* *
330766 CTTACTCCCTGAAGAAATAGAGAGC-GAGCCCATAGGAAGAAT
66 CTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
330808 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* *
330873 CTTACTCCCTGAAGAAATAGAGAGC-GAGCTCGTAGGAAGAAT
66 CTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* * *
330915 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGATAGCAGACCCGTAGGAAGATTATTGTTGGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
330980 TC-TACTCCCTGAAGAAATAGGGAGC
65 TCTTACTCCCTGAAGAAATAGAGAGC
331005 AAATACGATT
Statistics
Matches: 984, Mismatches: 51, Indels: 24
0.93 0.05 0.02
Matches are distributed among these distances:
104 2 0.00
105 224 0.23
106 106 0.11
107 601 0.61
108 51 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (107 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:330750 original size:372 final size:374
Alignment explanation
Indices: 329852--330996 Score: 1862
Period size: 372 Copynumber: 3.1 Consensus size: 374
329842 GCAACAGAAG
* * *
329852 ATTGTTCGAGTTCTACTCCCTGAAGAAATA-TG-GTGGACCCGTAGGAAGATTATTTTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTATTCGAGTT
*
329915 CTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTG
66 CTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
* *
329979 AAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAG
130 AAGAAATAGAGAGCGGACCCATAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAG
* * *
330044 AGAGAGCCTGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTA
195 AGCGAGCCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTA
*
330109 GGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATT
260 GGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATT
* * *
330174 GTTCGAGCTCTACTCCCTGAAGAAATAG-G-GTGGACCCGGAGGAAGATT
325 GTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330222 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTATTCGAGT
* *
330287 TC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGAAAGATTATTGTTCGAGTTTTACTCCCTG
65 TCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
*
330351 AAGAAATAGAGAGCGGA-CCAGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGA
130 AAGAAATAGAGAGCGGACCCA-TAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGA
* *
330415 GAGCG-GACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACTCG
194 GAGCGAG-CCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCG
*
330479 TAGGAAGATTATTGTTCGAGTTCTTACTCCTTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTA
258 TAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTA
* *
330544 TTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCTGTAGGAAGATT
323 TTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330596 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTATTCGAGTT
*
330661 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
66 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
*
330726 AGAAATAG-G-GTGGACCCATAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGA
131 AGAAATAGAGAGCGGACCCATAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGA
*
330789 GCGAGCCCATAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTAG
196 GCGAGCCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTAG
* * *
330854 GAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCTCGTAGGAAGAATATT
261 GAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGGAAGATTATT
* * *
330918 GTTCGAGTTCTTACTCCCTGAAGAAAAAGATAGCAGACCCGTAGGAAGATT
325 GTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
330969 ATTGTTGGAGTTCTACTCCCTGAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
330997 TAGGGAGCAA
Statistics
Matches: 721, Mismatches: 41, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
370 13 0.02
371 21 0.03
372 437 0.61
373 153 0.21
374 97 0.13
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (374 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTATTCGAGTT
CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
AGAAATAGAGAGCGGACCCATAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGA
GCGAGCCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACTCGTAG
GAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
TTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:331026 original size:53 final size:54
Alignment explanation
Indices: 330969--331086 Score: 123
Period size: 55 Copynumber: 2.2 Consensus size: 54
330959 TAGGAAGATT
* * * *
330969 ATTGTTGGAG-TTCTACTCCCTG-AAGAAATAGGGAGCAAATACGATTGTTGAAG
1 ATTGTTCGAGCTTATACTCCCTGAAAG-AATAGAGAGCAAAGACGATTGTTGAAG
* * * *
331022 ATTGTTCGAGTCTTATACTCTCTGAAAGCATAGAGAGCAGAGACGTTTGTTGAAG
1 ATTGTTCGAG-CTTATACTCCCTGAAAGAATAGAGAGCAAAGACGATTGTTGAAG
*
331077 ATTGTGCGAG
1 ATTGTTCGAG
331087 TTTCATGCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 9 0.17
55 41 0.77
56 3 0.06
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (54 bp):
ATTGTTCGAGCTTATACTCCCTGAAAGAATAGAGAGCAAAGACGATTGTTGAAG
Found at i:337262 original size:3 final size:3
Alignment explanation
Indices: 337254--337306 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
337244 ATTTATTTTG
* *
337254 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
337302 TAA TA
1 TAA TA
337307 TGTCTCGGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:342531 original size:22 final size:22
Alignment explanation
Indices: 342502--342563 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
342492 GAAGCACTAC
342502 TACTAAAGTGCCTTAGCATTGA
1 TACTAAAGTGCCTTAGCATTGA
** *
342524 TA-TAAAAGTGAATTTGCATTGA
1 TACT-AAAGTGCCTTAGCATTGA
*
342546 TACTAAAGTTCCTTAGCA
1 TACTAAAGTGCCTTAGCA
342564 CCGATGAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (22 bp):
TACTAAAGTGCCTTAGCATTGA
Found at i:344504 original size:121 final size:120
Alignment explanation
Indices: 344301--344519 Score: 280
Period size: 121 Copynumber: 1.8 Consensus size: 120
344291 ACCTAAAATT
* * * *
344301 TTTTGGCAATTTATTGAAGCAAATAATTAAATTGAAACTTAATGCATAAAGACGAGGGCCAAATA
1 TTTTAGCAATTTATTGAAGCAAATAATTAAATGGAAACATAA-GCATAAAGACGAGGACCAAATA
*
344366 AAAAATTCACCTAAATTAAAGGACTAAGGTGAAGACTCTAATTTTAACCTGACCAA
65 AAAAATTCACCTAAATTAAAAGACTAAGGTGAAGACTCTAATTTTAACCTGACCAA
* * *
344422 TTTTAGCAATTTATTGAATCAAATAATTAAGATGGAACCAT-AGACATAAA-AGTGAGGACCAAA
1 TTTTAGCAATTTATTGAAGCAAATAATTAA-ATGGAAACATAAG-CATAAAGA-CGAGGACCAAA
* * * *
344485 TTAAAGATTCCCCTTAATTAAAAGACTAAGGTGAA
63 TAAAAAATTCACCTAAATTAAAAGACTAAGGTGAA
344520 ATTAAACATA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
120 2 0.02
121 74 0.89
122 7 0.08
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (120 bp):
TTTTAGCAATTTATTGAAGCAAATAATTAAATGGAAACATAAGCATAAAGACGAGGACCAAATAA
AAAATTCACCTAAATTAAAAGACTAAGGTGAAGACTCTAATTTTAACCTGACCAA
Found at i:344763 original size:138 final size:138
Alignment explanation
Indices: 344390--344922 Score: 574
Period size: 139 Copynumber: 3.8 Consensus size: 138
344380 ATTAAAGGAC
* * * * *
344390 TAAGGTGAAGACTCTAAT-TTTAACCTGACCAATTTTAGCAATTTATTGAATCAAATAATTAAGA
1 TAAGATGAAGACTCTAATATTAAACCTAACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
* * *
344454 TGGAACCAT--AGACATAAAAGTGAGGACCAAATTAAAGATTCCCCTTAATTAAAAGACTAAGGT
66 TGGAACC-TCGAGA-ATAAAAGTGAGGACCAAATTAAA-ATTCTCCTAAATTAAAGGACTAAGGT
344517 GAAATTAAACA
128 GAAATTAAACA
* * * * * *
344528 TAAGATGAAGGCTCTAATATTAAACCCAATCAATTTTAAAAAATTATTTAATCAAATAATTAAAA
1 TAAGATGAAGACTCTAATATTAAACCTAACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
* * * ** *
344593 TGGAACATCGGGTATAAAAGTGAGGATAAAATTAAGAATTATCCTAAATTAAAGGACTAAGGTGA
66 TGGAACCTCGAGAATAAAAGTGAGGACCAAATTAA-AATTCTCCTAAATTAAAGGACTAAGGTGA
*
344658 AATTAAACC
130 AATTAAACA
** * * * *
344667 TAAGGCGAAGACTCAAATATT-AGCCTAGCCAATTTTAACAATTTATTGAATCGAATAATTAAAA
1 TAAGATGAAGACTCTAATATTAAACCTAACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
* * * * * *
344731 TGGAACCTCGGGAATAAAAGTGAGAATCAAATTAAAATTTCTACTAAATTAAAGGACTAAGATAA
66 TGGAACCTCGAGAATAAAAGTGAGGACCAAATTAAAA-TTCTCCTAAATTAAAGGACTAAGGTGA
344796 AATTAAACA
130 AATTAAACA
* **** *
344805 TAAGATAAAGACTCTAATATTAAACCTAATTGGTTTTAGTA-AATTTCTT-AATCAAATAATTAA
1 TAAGATGAAGACTCTAATATTAAACCTAACCAATTTTA--ACAATTTATTGAATCAAATAATTAA
* * *
344868 TATGGAACCTCGAGCATAAAAGAGAGGACCAAATTAAAAATTCTCCTAAATTAAA
64 AATGGAACCTCGAGAATAAAAGTGAGGACCAAATT-AAAATTCTCCTAAATTAAA
344923 CTATGTTTAG
Statistics
Matches: 325, Mismatches: 61, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
137 2 0.01
138 131 0.40
139 178 0.55
140 13 0.04
141 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (138 bp):
TAAGATGAAGACTCTAATATTAAACCTAACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
TGGAACCTCGAGAATAAAAGTGAGGACCAAATTAAAATTCTCCTAAATTAAAGGACTAAGGTGAA
ATTAAACA
Found at i:344904 original size:277 final size:277
Alignment explanation
Indices: 344389--344922 Score: 691
Period size: 277 Copynumber: 1.9 Consensus size: 277
344379 AATTAAAGGA
* * * * *
344389 CTAAGGTGAAGACTCTAATTTTAACCTGACCAATTTTAGCAATTTATTGAATCAAATAATTAAGA
1 CTAAGGCGAAGACTCAAATATTAACCTGACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
* * * * *
344454 TGGAACCATAGACATAAAAGTGAGGACCAAATTAAAGATTCCCCTTAATTAAAAGACTAAGGTGA
66 TGGAACCATAGACATAAAAGTGAGAACCAAATTAAAGATTCCACTAAATTAAAAGACTAAGATAA
* *
344519 AATTAAACATAAGATGAAGGCTCTAATATTAAACCCAATCAATTTTAAAAAATTATTTAATCAAA
131 AATTAAACATAAGATAAAGACTCTAATATTAAACCCAATCAATTTTAAAAAATTATTTAATCAAA
* * * * *
344584 TAATTAAAATGGAACATCGGGTATAAAAGTGAGGATAAAATTAAGAATTATCCTAAATTAAAGGA
196 TAATTAAAATGGAACATCGAGCATAAAAGAGAGGACAAAATTAAAAATTATCCTAAATTAAAGGA
344649 CTAAGGTGAAATTAAAC
261 CTAAGGTGAAATTAAAC
* *
344666 CTAAGGCGAAGACTCAAATATTAGCCT-AGCCAATTTTAACAATTTATTGAATCGAATAATTAAA
1 CTAAGGCGAAGACTCAAATATTAACCTGA-CCAATTTTAACAATTTATTGAATCAAATAATTAAA
* * * *
344730 ATGGAACC-TCGGGA-ATAAAAGTGAGAATCAAATTAAA-ATTTCTACTAAATTAAAGGACTAAG
65 ATGGAACCAT--AGACATAAAAGTGAGAACCAAATTAAAGA-TTCCACTAAATTAAAAGACTAAG
* *** **
344792 ATAAAATTAAACATAAGATAAAGACTCTAATATTAAACCTAATTGGTTTTAGTAAATT-TCTTAA
127 ATAAAATTAAACATAAGATAAAGACTCTAATATTAAACCCAATCAATTTTAAAAAATTAT-TTAA
* * * *
344856 TCAAATAATTAATATGGAACCTCGAGCATAAAAGAGAGGACCAAATTAAAAATTCTCCTAAATTA
191 TCAAATAATTAAAATGGAACATCGAGCATAAAAGAGAGGACAAAATTAAAAATTATCCTAAATTA
344921 AA
256 AA
344923 CTATGTTTAG
Statistics
Matches: 219, Mismatches: 33, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
276 4 0.02
277 213 0.97
278 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (277 bp):
CTAAGGCGAAGACTCAAATATTAACCTGACCAATTTTAACAATTTATTGAATCAAATAATTAAAA
TGGAACCATAGACATAAAAGTGAGAACCAAATTAAAGATTCCACTAAATTAAAAGACTAAGATAA
AATTAAACATAAGATAAAGACTCTAATATTAAACCCAATCAATTTTAAAAAATTATTTAATCAAA
TAATTAAAATGGAACATCGAGCATAAAAGAGAGGACAAAATTAAAAATTATCCTAAATTAAAGGA
CTAAGGTGAAATTAAAC
Found at i:345204 original size:16 final size:15
Alignment explanation
Indices: 345151--345205 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
345141 TATAGGACTG
345151 AAATTAAAAGG-CAT
1 AAATTAAAAGGACAT
*
345165 AAATT-AAAGGTACTAA
1 AAATTAAAAGG-AC-AT
345181 AAATTAAAAGGACAT
1 AAATTAAAAGGACAT
345196 AAATGTAAAA
1 AAAT-TAAAA
345206 TACCATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.15
14 5 0.15
15 6 0.18
16 13 0.38
17 5 0.15
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (15 bp):
AAATTAAAAGGACAT
Found at i:348452 original size:7 final size:8
Alignment explanation
Indices: 348439--348476 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
348429 TATTTTCATT
348439 ATTTTTTC
1 ATTTTTTC
348447 -TTTTTTC
1 ATTTTTTC
348454 ATTTTTTTC
1 A-TTTTTTC
348463 A-TTTTTC
1 ATTTTTTC
348470 ATTTTTT
1 ATTTTTT
348477 TCCTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 14 0.52
8 5 0.19
9 8 0.30
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
ATTTTTTC
Found at i:348459 original size:16 final size:16
Alignment explanation
Indices: 348440--348483 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
348430 ATTTTCATTA
348440 TTTTTTCTTTTTTCAT
1 TTTTTTCTTTTTTCAT
*
348456 TTTTTTCATTTTTCAT
1 TTTTTTCTTTTTTCAT
348472 TTTTTTCCTTTT
1 TTTTTT-CTTTT
348484 CTTCTCCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTTTCAT
Found at i:348477 original size:9 final size:9
Alignment explanation
Indices: 348447--348483 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
348437 TTATTTTTTC
348447 TTTTTTCAT
1 TTTTTTCAT
348456 TTTTTTCA-
1 TTTTTTCAT
348464 -TTTTTCAT
1 TTTTTTCAT
*
348472 TTTTTTCCT
1 TTTTTTCAT
348481 TTT
1 TTT
348484 CTTCTCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:363150 original size:30 final size:30
Alignment explanation
Indices: 363116--363180 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
363106 CTGTTTTAGC
* * *
363116 TATTTTAGTCCTTTTAGTTTATGTATCTAT
1 TATTTTACTCCTTTAACTTTATGTATCTAT
* * *
363146 TATTTTTCTCCTTTAACTTTATGTCTTTAT
1 TATTTTACTCCTTTAACTTTATGTATCTAT
363176 TATTT
1 TATTT
363181 GGCCCTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.63
Consensus pattern (30 bp):
TATTTTACTCCTTTAACTTTATGTATCTAT
Found at i:363578 original size:176 final size:179
Alignment explanation
Indices: 363284--363638 Score: 689
Period size: 176 Copynumber: 2.0 Consensus size: 179
363274 TTAGTCATTT
363284 ATGTATGAATGTATTTTACATATTATGTGGTTATTTATCTTATGTAAATAATGTTTTTAGTTCCA
1 ATGTATGAATGTATTTTACATATTATGTGGTTATTTATCTTATGTAAATAATGTTTTTAGTTCCA
363349 TTTAATGTAAACATTTTATTCTATATTTTTAATTACATTTATTTCTATTACATTTTATCCATGGA
66 TTTAATGTAAACATTTTATTCTATATTTTTAATTACATTTATTTCTATTACATTTTATCCATGGA
363414 TGAAA-ATTTGATTTTTA-TTCT-AGAACACGTATACGTAAATTGAGCG
131 TGAAATATTTGATTTTTATTTCTAAGAACACGTATACGTAAATTGAGCG
363460 ATGTATGAATGTATTTTACATATTATGTGGTTATTTATCTTATGTAAATAATGTTTTTAGTTCCA
1 ATGTATGAATGTATTTTACATATTATGTGGTTATTTATCTTATGTAAATAATGTTTTTAGTTCCA
363525 TTTAATGTAAACATTTTATTCTATATTTTTAATTACATTTATTTCTATTACATTTTATCCATGGA
66 TTTAATGTAAACATTTTATTCTATATTTTTAATTACATTTATTTCTATTACATTTTATCCATGGA
363590 TGAAATATTTGATTTTTATTTCTAAGAACACGTATACGTAAATTGAGCG
131 TGAAATATTTGATTTTTATTTCTAAGAACACGTATACGTAAATTGAGCG
363639 TGGAAAGTAC
Statistics
Matches: 176, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
176 135 0.77
177 12 0.07
178 4 0.02
179 25 0.14
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (179 bp):
ATGTATGAATGTATTTTACATATTATGTGGTTATTTATCTTATGTAAATAATGTTTTTAGTTCCA
TTTAATGTAAACATTTTATTCTATATTTTTAATTACATTTATTTCTATTACATTTTATCCATGGA
TGAAATATTTGATTTTTATTTCTAAGAACACGTATACGTAAATTGAGCG
Found at i:369708 original size:14 final size:14
Alignment explanation
Indices: 369691--369718 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
369681 ACCTGACCTA
369691 TTGAATTTGACCCG
1 TTGAATTTGACCCG
369705 TTGAATTTGACCCG
1 TTGAATTTGACCCG
369719 ACCTGTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TTGAATTTGACCCG
Found at i:369721 original size:19 final size:19
Alignment explanation
Indices: 369699--369735 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
369689 TATTGAATTT
369699 GACCCGTTGAATTTGACCC
1 GACCCGTTGAATTTGACCC
* *
369718 GACCTGTTGACTTTGACC
1 GACCCGTTGAATTTGACC
369736 TAACTCGTCG
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:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (19 bp):
GACCCGTTGAATTTGACCC
Found at i:379341 original size:77 final size:77
Alignment explanation
Indices: 379214--379368 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
379204 CTCCACCAGA
379214 TCGTCTACAATCATTCAAAGATTGAAATATTTCTACTAGAATAGTCAGGGCAGGATTTATTCTCT
1 TCGTCTACAATCATTCAAAGATTGAAATATTTCTACTAGAATAGTCAGGGCAGGATTTATTCTCT
379279 TCTATAAAACTT
66 TCTATAAAACTT
379291 TCGTCTACAATCATTCAAAGATTGAAATATTTCTACTAGAATAGTCAGGGCAGGATTTATTCTCT
1 TCGTCTACAATCATTCAAAGATTGAAATATTTCTACTAGAATAGTCAGGGCAGGATTTATTCTCT
379356 TCTATAAAACTT
66 TCTATAAAACTT
379368 T
1 T
379369 AAACAAAACT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.37
Consensus pattern (77 bp):
TCGTCTACAATCATTCAAAGATTGAAATATTTCTACTAGAATAGTCAGGGCAGGATTTATTCTCT
TCTATAAAACTT
Found at i:381624 original size:139 final size:137
Alignment explanation
Indices: 381396--382116 Score: 783
Period size: 139 Copynumber: 5.2 Consensus size: 137
381386 AACCTAAAGG
** * * * * * * * *
381396 ATTAAACCTAAAATGTAGGCTTTGATATTAACCTAATCAGTTTTAGTAATTTATTGAATCAAATA
1 ATTAAACCTAAGGTGAAGGCTCTAATATTAACCTGACCAATTTTA-CAATTTATTGAATCGAATA
* * * * *
381461 ATTTAAATGGAACTTTGGGTATAAAAGCTA-GACCAAATAAGAAAATTCACCTAAATTAAAGGAC
65 ATTAAAATGGAACCTAGGGCATAAAAGCTAGGACCAAATAA-AAAATTCTCCTAAATTAAAGGAC
381525 TAAGGTGAA
129 TAAGGTGAA
* * *
381534 ATTAAA-CTCAAGGTGAAGGCT-TGAATATATAATGCTTATCAATTTTACAATTTATTGAATCGA
1 ATTAAACCT-AAGGTGAAGGCTCT-AATAT-TAA-CCTGACCAATTTTACAATTTATTGAATCGA
* * * *
381597 ATAAATAAAATTGAACCTAGGGCATAAAATC-ATGGACCAAATAAAAAATTCACCTAAATTAAAG
62 ATAATTAAAATGGAACCTAGGGCATAAAAGCTA-GGACCAAATAAAAAATTCTCCTAAATTAAAG
*
381661 GATTAAGGTGAA
126 GACTAAGGTGAA
* *
381673 ACTAAACCTAAGGTGAAGGCTCT-ATATTAACCTGGCCAATTTTAGCAATTTATTGAATCGAATA
1 ATTAAACCTAAGGTGAAGGCTCTAATATTAACCTGACCAATTTTA-CAATTTATTGAATCGAATA
* *
381737 ATTAAAATGGAACCTTGGGCATAAAAGCAAGGACCAAA-ATAAAAATTCTCCTAAATTAAAGGAC
65 ATTAAAATGGAACCTAGGGCATAAAAGCTAGGACCAAATA-AAAAATTCTCCTAAATTAAAGGAC
381801 TAAGGTGAA
129 TAAGGTGAA
* * * * * * * * **
381810 ATTAAATCTAAGATGAAGTCTTTAATATTAAACCTAATCAATTTTAACAAATTATTTAATTAAAT
1 ATTAAACCTAAGGTGAAGGCTCTAATATT-AACCTGACCAATTTT-ACAATTTATTGAATCGAAT
* * * * * * *
381875 AATTAAAATGGAACATAGGGCATAAAAACGATGATCAAATTAAAAATTCTCCTAAATTAAAAGAC
64 AATTAAAATGGAACCTAGGGCATAAAAGCTAGGACCAAATAAAAAATTCTCCTAAATTAAAGGAC
381940 TAAGGTGAA
129 TAAGGTGAA
* *
381949 ATTAAACCTAAGGTGAAGGCTCTAATATTAACCTGACCAATTTTACTAATTTAATGAATTGAATA
1 ATTAAACCTAAGGTGAAGGCTCTAATATTAACCTGACCAATTTTAC-AATTTATTGAATCGAATA
** * * * * *
382014 ATTAAAATATAACCTA-TGTATAAAAG-TGAGGACTAAATTAAAAATTCTCCTACATTAAAGGAC
65 ATTAAAATGGAACCTAGGGCATAAAAGCT-AGGACCAAATAAAAAATTCTCCTAAATTAAAGGAC
382077 TAAGGTGAA
129 TAAGGTGAA
*
382086 ATTAAACCTAAGATGAAGGCTCTAATATTAA
1 ATTAAACCTAAGGTGAAGGCTCTAATATTAA
382117 ACCTAAGATG
Statistics
Matches: 495, Mismatches: 71, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
136 11 0.02
137 184 0.37
138 70 0.14
139 205 0.41
140 25 0.05
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (137 bp):
ATTAAACCTAAGGTGAAGGCTCTAATATTAACCTGACCAATTTTACAATTTATTGAATCGAATAA
TTAAAATGGAACCTAGGGCATAAAAGCTAGGACCAAATAAAAAATTCTCCTAAATTAAAGGACTA
AGGTGAA
Found at i:381922 original size:276 final size:275
Alignment explanation
Indices: 381420--382122 Score: 898
Period size: 276 Copynumber: 2.5 Consensus size: 275
381410 GTAGGCTTTG
* * * * * * *
381420 ATATTAACCTAATCAGTTTTAGTAATTTATTGAATCAAATAATTTAAATGGAACTTTGGGTATAA
1 ATATTAACCTGACCAATTTTAGCAATTTATTGAATCGAATAATTAAAATGGAACCTTGGGTATAA
* * *
381485 AAGCTA-GACC-AAATAAGAAAATTCACCTAAATTAAAGGACTAAGGTGAAATTAAACTCAAGGT
66 AAGCAAGGACCAAAAT-A-AAAATTCTCCTAAATTAAAGGACTAAGGTGAAATTAAACT-AAGAT
* ** * * * *
381548 GAAGGCTTGAATATATAATGCTTATCAATTTTACAATTTATTGAATCGAATAAATAAAATTGAAC
128 GAAGGCTTTAATAT-TAAACCTAATCAATTTTACAAATTATTGAATCAAATAAATAAAATGGAAC
* * * *
381613 CTAGGGCATAAAATCATGGACCAAATAAAAAATTCACCTAAATTAAAGGATTAAGGTGAAACTAA
192 ATAGGGCATAAAAACATGGACCAAATAAAAAATTCACCTAAATTAAAAGACTAAGGTGAAACTAA
381678 ACCTAAGGTGAAGGCTCT-
257 ACCTAAGGTGAAGGCTCTA
* *
381696 ATATTAACCTGGCCAATTTTAGCAATTTATTGAATCGAATAATTAAAATGGAACCTTGGGCATAA
1 ATATTAACCTGACCAATTTTAGCAATTTATTGAATCGAATAATTAAAATGGAACCTTGGGTATAA
381761 AAGCAAGGACCAAAATAAAAATTCTCCTAAATTAAAGGACTAAGGTGAAATTAAATCTAAGATGA
66 AAGCAAGGACCAAAATAAAAATTCTCCTAAATTAAAGGACTAAGGTGAAATTAAA-CTAAGATGA
* * * *
381826 AGTCTTTAATATTAAACCTAATCAATTTTAACAAATTATTTAATTAAATAATTAAAATGGAACAT
130 AGGCTTTAATATTAAACCTAATCAATTTT-ACAAATTATTGAATCAAATAAATAAAATGGAACAT
* * * *
381891 AGGGCATAAAAACGAT-GATCAAATTAAAAATTCTCCTAAATTAAAAGACTAAGGTGAAATTAAA
194 AGGGCATAAAAAC-ATGGACCAAATAAAAAATTCACCTAAATTAAAAGACTAAGGTGAAACTAAA
381955 CCTAAGGTGAAGGCTCTA
258 CCTAAGGTGAAGGCTCTA
* * **
381973 ATATTAACCTGACCAATTTTA-CTAATTTAATGAATTGAATAATTAAAATATAACCTAT--GTAT
1 ATATTAACCTGACCAATTTTAGC-AATTTATTGAATCGAATAATTAAAATGGAACCT-TGGGTAT
** * * *
382035 AAAAGTGAGGACTAAATTAAAAATTCTCCTACATTAAAGGACTAAGGTGAAATTAAACCTAAGAT
64 AAAAGCAAGGACCAAAATAAAAATTCTCCTAAATTAAAGGACTAAGGTGAAATTAAA-CTAAGAT
*
382100 GAAGGCTCTAATATTAAACCTAA
128 GAAGGCTTTAATATTAAACCTAA
382123 GATGAAGGCT
Statistics
Matches: 374, Mismatches: 45, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
275 14 0.04
276 297 0.79
277 58 0.16
278 5 0.01
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (275 bp):
ATATTAACCTGACCAATTTTAGCAATTTATTGAATCGAATAATTAAAATGGAACCTTGGGTATAA
AAGCAAGGACCAAAATAAAAATTCTCCTAAATTAAAGGACTAAGGTGAAATTAAACTAAGATGAA
GGCTTTAATATTAAACCTAATCAATTTTACAAATTATTGAATCAAATAAATAAAATGGAACATAG
GGCATAAAAACATGGACCAAATAAAAAATTCACCTAAATTAAAAGACTAAGGTGAAACTAAACCT
AAGGTGAAGGCTCTA
Found at i:382116 original size:26 final size:26
Alignment explanation
Indices: 382086--382148 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
382076 CTAAGGTGAA
382086 ATTAAACCTAAGATGAAGGCTCTAAT
1 ATTAAACCTAAGATGAAGGCTCTAAT
382112 ATTAAACCTAAGATGAAGGCTCTAAT
1 ATTAAACCTAAGATGAAGGCTCTAAT
382138 ATTAAACCTAA
1 ATTAAACCTAA
382149 TCGATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (26 bp):
ATTAAACCTAAGATGAAGGCTCTAAT
Found at i:386693 original size:14 final size:14
Alignment explanation
Indices: 386666--386718 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
386656 CTAACTAATG
* *
386666 AAATCATAAAAAAT
1 AAATTATAAAAACT
* *
386680 AAATTATATCAAATT
1 AAATTATA-AAAACT
*
386695 AAAGTATAAAAACT
1 AAATTATAAAAACT
386709 AAATTATAAA
1 AAATTATAAA
386719 TTTGATATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (14 bp):
AAATTATAAAAACT
Found at i:389013 original size:30 final size:30
Alignment explanation
Indices: 388979--389041 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
388969 CCGCTAATAA
*
388979 ATTGGCATAATTATATATTTGGTCTTTAAT
1 ATTGGCATAATTATATATTTGGTCCTTAAT
389009 ATTGGCATAATTATATATTTGGTCCTTAAT
1 ATTGGCATAATTATATATTTGGTCCTTAAT
389039 ATT
1 ATT
389042 TATATATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTGGCATAATTATATATTTGGTCCTTAAT
Found at i:389026 original size:16 final size:16
Alignment explanation
Indices: 388979--389027 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
388969 CCGCTAATAA
388979 ATTGGCATAATTATAT
1 ATTGGCATAATTATAT
388995 ATTTGGTC-T--TTA-AT
1 A-TTGG-CATAATTATAT
389009 ATTGGCATAATTATAT
1 ATTGGCATAATTATAT
389025 ATT
1 ATT
389028 TGGTCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
12 1 0.04
13 5 0.19
14 3 0.11
15 6 0.22
16 6 0.22
17 5 0.19
18 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (16 bp):
ATTGGCATAATTATAT
Found at i:389391 original size:20 final size:20
Alignment explanation
Indices: 389358--389408 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 20
389348 TGATAAAACC
*
389358 TTAAACAAATTATT-TGT--
1 TTAAACAAATTATTATTTAA
389375 TTAAACAAATTATTATTTAA
1 TTAAACAAATTATTATTTAA
*
389395 TTAAATAAATTATT
1 TTAAACAAATTATT
389409 CACGACTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAACAAATTATTATTTAA
Found at i:389533 original size:29 final size:29
Alignment explanation
Indices: 389496--389559 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
389486 ATCGAACCAA
* **
389496 AATTTATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
*
389525 AATTAATTTGGAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
389554 AATTAA
1 AATTAA
389560 CCTAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCAAACCG
Found at i:389903 original size:29 final size:29
Alignment explanation
Indices: 389866--389929 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
389856 ATCGAACCAA
*
389866 AATTTATTTGAAAAGTATTAACCGAACCG
1 AATTAATTTGAAAAGTATTAACCGAACCG
* *
389895 AATTAATTTGAAAATTATTAACCGGACCG
1 AATTAATTTGAAAAGTATTAACCGAACCG
389924 AATTAA
1 AATTAA
389930 CCGGTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (29 bp):
AATTAATTTGAAAAGTATTAACCGAACCG
Found at i:390131 original size:17 final size:17
Alignment explanation
Indices: 390109--390155 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
390099 TAATTTAAAT
390109 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
390126 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
390143 AATAATTTGTTTA
1 AATAATTTGTTTA
390156 CTTTTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (17 bp):
AATAATTTGTTTAAACA
Done.