Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
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: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 7 of 9
Found at i:931307 original size:29 final size:31
Alignment explanation
Indices: 931257--931317 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
931247 TTTTTTTATT
*
931257 TACTACAATTTAAAAAATACAATAACTAAAA
1 TACTACAATTTAAAAAATACAAAAACTAAAA
* *
931288 TACTA-AATTT-AATAATACAAAAATTAAAA
1 TACTACAATTTAAAAAATACAAAAACTAAAA
931317 T
1 T
931318 TCTTTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
30 5 0.19
31 5 0.19
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.30
Consensus pattern (31 bp):
TACTACAATTTAAAAAATACAAAAACTAAAA
Found at i:931756 original size:2 final size:2
Alignment explanation
Indices: 931700--931739 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
931690 TAGGATGTTA
931700 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
931740 GACAATGGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:934530 original size:16 final size:16
Alignment explanation
Indices: 934499--934545 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
934489 TTTAAAAATT
934499 TTTGGGTCATTTTCGAG
1 TTTGGGTCA-TTTCGAG
934516 TTTGGGTCATTTCGAG
1 TTTGGGTCATTTCGAG
* *
934532 TTCGGATCATTTCG
1 TTTGGGTCATTTCG
934546 GGTTCAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (16 bp):
TTTGGGTCATTTCGAG
Found at i:934640 original size:15 final size:15
Alignment explanation
Indices: 934620--934650 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
934610 TTCTCGATTC
934620 AGGTCAATTGTGTTT
1 AGGTCAATTGTGTTT
934635 AGGTCAATTGTGTTT
1 AGGTCAATTGTGTTT
934650 A
1 A
934651 ACATTCGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (15 bp):
AGGTCAATTGTGTTT
Found at i:935758 original size:18 final size:18
Alignment explanation
Indices: 935717--935759 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
935707 AGTTCGTATT
* *
935717 TTATTTA-ATTTAATTTG
1 TTATTTATATTTAAATTA
*
935734 TTTTTTATATTTAAATTA
1 TTATTTATATTTAAATTA
935752 TTATTTAT
1 TTATTTAT
935760 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTATATTTAAATTA
Found at i:935807 original size:21 final size:21
Alignment explanation
Indices: 935781--935821 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
935771 TATTTAAAAA
935781 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
935802 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
935822 AATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:935847 original size:20 final size:19
Alignment explanation
Indices: 935818--935858 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
935808 TATAATTAAA
*
935818 TTTAAATAAAAATTTATTAT
1 TTTAAATAAAAA-ATATTAT
*
935838 TTTAATTAAAAAATATTAT
1 TTTAAATAAAAAATATTAT
935857 TT
1 TT
935859 CGAATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAATAAAAAATATTAT
Found at i:935985 original size:3 final size:3
Alignment explanation
Indices: 935977--936006 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
935967 AAAAACTAAA
935977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
936007 CTAGTAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:938222 original size:13 final size:13
Alignment explanation
Indices: 938214--938239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
938204 CTGAAAGAAG
938214 AGAGAGAAAAAAA
1 AGAGAGAAAAAAA
938227 AGAGAGAAAAAAA
1 AGAGAGAAAAAAA
938240 GAAAAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAGAGAAAAAAA
Found at i:938236 original size:11 final size:11
Alignment explanation
Indices: 938216--938250 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
938206 GAAAGAAGAG
938216 AGAGAAAAAAA
1 AGAGAAAAAAA
*
938227 AGAGAGAAAAA
1 AGAGAAAAAAA
938238 A-AGAAAAAAA
1 AGAGAAAAAAA
938248 AGA
1 AGA
938251 AAATTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAGAAAAAAA
Found at i:939212 original size:5 final size:5
Alignment explanation
Indices: 939202--939226 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
939192 GATATTTTCA
939202 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
939227 TGGTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:939280 original size:149 final size:144
Alignment explanation
Indices: 939101--939460 Score: 422
Period size: 149 Copynumber: 2.5 Consensus size: 144
939091 GTATTTTTTC
*
939101 TAATCTTTTATATTCTTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATTCT
1 TAATCTTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATTCT
* * * **
939166 TTCGAGTTTCCATTAGGGTGCAAAAT-GATATTTTCAAAAATAAAATAAAATAAAATAAAATTGG
66 TTCGAGTCTCCATTAGGATACAAAATAG-TATTTTCAAAAAT--AATAAAATAAAATAAAATTAA
*
939230 TATTATTAG-GATAAATTT
128 TACT-TTAGAGA-AAATTT
*
939248 TAATTTTTTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAACCTTTTCGTAT
1 TAA--TCTTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAA-CTTTTCGTAT
* * * ** **
939313 TCTATCGGGTCTCCATTAGGATACGAAATAGTATTTTCAAAAATAATAAAATTGAATTGAATTAA
63 TCTTTCGAGTCTCCATTAGGATACAAAATAGTATTTTCAAAAATAATAAAATAAAATAAAATTAA
*
939378 TACTTTCGAGAAAATTT
128 TACTTTAGAGAAAATTT
* ** * *
939395 TAATCTTTTATATTCCTAT-AAGCATCAATCGAGGTATAAAAGATTTCAAAAACTTTTCGTA-TC
1 TAATCTTTTATATTCCTATGGA-CATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATTC
939458 TTT
65 TTT
939461 TTGAGCTTTT
Statistics
Matches: 184, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
143 4 0.02
144 10 0.05
145 41 0.22
147 15 0.08
148 20 0.11
149 47 0.26
150 46 0.25
151 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Consensus pattern (144 bp):
TAATCTTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATTCT
TTCGAGTCTCCATTAGGATACAAAATAGTATTTTCAAAAATAATAAAATAAAATAAAATTAATAC
TTTAGAGAAAATTT
Found at i:940960 original size:15 final size:15
Alignment explanation
Indices: 940942--940976 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
940932 TGATCATGTG
940942 TTAATTAAATTTTAA
1 TTAATTAAATTTTAA
**
940957 TTAATTCGATTTTAA
1 TTAATTAAATTTTAA
940972 TTAAT
1 TTAAT
940977 GTTCAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TTAATTAAATTTTAA
Found at i:941815 original size:20 final size:20
Alignment explanation
Indices: 941792--941959 Score: 120
Period size: 20 Copynumber: 7.8 Consensus size: 20
941782 ACGTACCTAG
941792 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
941812 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
941832 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
941852 ATATATCGATATATTCTATCCTTTTACCCA
1 ATGTATCG--ATA--C-AT--TTTT---CA
*
941882 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTTTTCA
* * *
941903 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
941923 ATGTCTCAATACGTTCTTCA
1 ATGTATCGATACATTTTTCA
941943 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
941960 GTCTTTTTAC
Statistics
Matches: 111, Mismatches: 26, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
20 82 0.74
21 2 0.02
22 3 0.03
24 4 0.04
25 2 0.02
26 2 0.02
27 4 0.04
29 3 0.03
30 2 0.02
31 7 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:941852 original size:40 final size:40
Alignment explanation
Indices: 941792--941956 Score: 159
Period size: 40 Copynumber: 3.9 Consensus size: 40
941782 ACGTACCTAG
*
941792 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
* * **
941832 ATGTATCGATACATTCTTCAATATATCGATATATTCTATCCTTTTACCCA
1 ATGTATCGATACATTCTTCAATGTATCG--ATA--C-A----TGTA-TGA
941882 GATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
1 -ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
* * *
941923 ATGTCTCAATACGTTCTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACAT
941957 TTTGTCTTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
40 57 0.56
41 1 0.01
42 6 0.06
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
49 6 0.06
50 1 0.01
51 27 0.26
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
Found at i:941950 original size:91 final size:91
Alignment explanation
Indices: 941785--942008 Score: 331
Period size: 91 Copynumber: 2.5 Consensus size: 91
941775 TATGGAAACG
*
941785 TACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTCTT
1 TACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTT
*
941850 CAATATATCGATATATTCTATCCTTT
66 CAATATATCGATACATTCTATCCTTT
* * * *
941876 TACCCAGATGTATCGATACATTCTTCAATGTATCGATACATGTATGAATGTCTCAATACGTTCTT
1 TACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTT
* * * *
941941 CAATGTATCGATACATTTTGTCTTTT
66 CAATATATCGATACATTCTATCCTTT
* *
941967 TACCTGGATGTATTCGATACATTTTTCAATATATCGATACAT
1 TACCTAGATGTA-TCGATACATTTTTCAATGTATCGATACAT
942009 CTAGTTAAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
91 91 0.77
92 27 0.23
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (91 bp):
TACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTT
CAATATATCGATACATTCTATCCTTT
Found at i:948250 original size:26 final size:25
Alignment explanation
Indices: 948212--948261 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
948202 ACTAGCTACA
* *
948212 TTTTGACTTGATATTGGTTTCAATAG
1 TTTTGACTCGATATT-ATTTCAATAG
948238 TTTTGACTCGATATTATTTCAATA
1 TTTTGACTCGATATTATTTCAATA
948262 TGATTCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (25 bp):
TTTTGACTCGATATTATTTCAATAG
Found at i:951304 original size:164 final size:163
Alignment explanation
Indices: 951119--951425 Score: 374
Period size: 164 Copynumber: 1.9 Consensus size: 163
951109 ATTTTCAAAG
* * * *
951119 AAAAATTCAAAACTCATGAAAATGAATTAATTTTTTA-AAACTGATTTAATAT-AAATCAAATGA
1 AAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAGAAA-GGATTTAATATAAAAT-AAATAA
* *
951182 TGATGTTTAATGAA-TTTTAAAA-ATTAAAACCAAGAAAAGTCCCCTC-GAAAAAA-TTACGGAG
64 TAATATTTAATGAATTTTTAAAATATTAAAACCAAGAAAA-TCCCCTCAGAAAAAATTTAC-GA-
*
951243 TAAAAAACACCGTATTTTGTAAAAAAAGAATTTCAGGGA
126 -AAAAAACACCGTAATTTGTAAAAAAAGAATTTCAGGGA
* *
951282 AAAAATTCAAAAATTTATGAAAATGAATGAATTTTTGAGAAAGGATTTAATATAAAATAAATAAT
1 AAAAATTC-AAAACTCATGAAAATGAATGAATTTTTGAGAAAGGATTTAATATAAAATAAATAAT
* * * * **
951347 AATATTTGATGAATTTTTAAAATTTTAAACCCATGAAAATCCTTTCAGAAAAAATTTACGAAAAA
65 AATATTTAATGAATTTTTAAAATATTAAAACCAAGAAAATCCCCTCAGAAAAAATTTACGAAAAA
951412 AACACCGTAATTTG
130 AACACCGTAATTTG
951426 AACACATGAG
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
163 8 0.07
164 68 0.56
165 20 0.16
166 22 0.18
167 4 0.03
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.31
Consensus pattern (163 bp):
AAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAGAAAGGATTTAATATAAAATAAATAATA
ATATTTAATGAATTTTTAAAATATTAAAACCAAGAAAATCCCCTCAGAAAAAATTTACGAAAAAA
ACACCGTAATTTGTAAAAAAAGAATTTCAGGGA
Found at i:952581 original size:21 final size:22
Alignment explanation
Indices: 952552--952594 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
952542 TTATATGAGA
* *
952552 TAAATTATATAATATATAATTA
1 TAAATTATAAATTATATAATTA
952574 TAAA-TATAAATTATATAATTA
1 TAAATTATAAATTATATAATTA
952595 AAAAATGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTATAAATTATATAATTA
Found at i:952596 original size:13 final size:14
Alignment explanation
Indices: 952551--952596 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
952541 TTTATATGAG
952551 ATAAATTATATAAT
1 ATAAATTATATAAT
952565 ATATAATTATA-AAT
1 ATA-AATTATATAAT
952579 ATAAATTATATAAT
1 ATAAATTATATAAT
952593 -TAAA
1 ATAAA
952597 AAATGAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.37
14 12 0.40
15 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATTATATAAT
Found at i:956013 original size:18 final size:18
Alignment explanation
Indices: 955990--956025 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
955980 AGATATATCA
955990 TTTTAAAT-TTATTATTAT
1 TTTTAAATATTA-TATTAT
956008 TTTTAAATATTATATTAT
1 TTTTAAATATTATATTAT
956026 ATATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAATATTATATTAT
Found at i:956025 original size:21 final size:23
Alignment explanation
Indices: 955999--956041 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
955989 ATTTTAAATT
*
955999 TATTAT-TATTTTTAA-ATATTA
1 TATTATATATTTATAATATATTA
956020 TATTATATATTTATAATATATT
1 TATTATATATTTATAATATATT
956042 TTCAAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATATATTTATAATATATTA
Found at i:956113 original size:2 final size:2
Alignment explanation
Indices: 956101--956135 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
956091 AAATTACATA
956101 AT AT A- 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
956136 GCAAACACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:956263 original size:13 final size:13
Alignment explanation
Indices: 956159--956273 Score: 52
Period size: 13 Copynumber: 9.4 Consensus size: 13
956149 TTAAGATTAT
*
956159 ATATTTTTAATAA
1 ATATATTTAATAA
956172 A-ATATTTAAATATA
1 ATATATTT-AATA-A
*
956186 ATA-A-AT-ATAA
1 ATATATTTAATAA
*
956196 AAATATTTAA-AA
1 ATATATTTAATAA
956208 ATATA--TAATAA
1 ATATATTTAATAA
*
956219 AT-TA-TTATTAA
1 ATATATTTAATAA
* * *
956230 TTAAATTCAAT-A
1 ATATATTTAATAA
956242 ATATAATTTAATAA
1 ATAT-ATTTAATAA
**
956256 ATATATTTTTTAA
1 ATATATTTAATAA
956269 ATATA
1 ATATA
956274 ATTGTAAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
10 8 0.11
11 14 0.19
12 16 0.21
13 28 0.37
14 8 0.11
15 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATTTAATAA
Found at i:956318 original size:21 final size:20
Alignment explanation
Indices: 956288--956352 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
956278 TAAAAAAGGA
956288 AAAAATATTAAAAATTAATTTT
1 AAAAA-ATT-AAAATTAATTTT
**
956310 AAAAAATT-AAATTAAAATT
1 AAAAAATTAAAATTAATTTT
*
956329 AAAAAATTTAAAATCTTATTTT
1 AAAAAA-TTAAAAT-TAATTTT
956351 AA
1 AA
956353 CTAATATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 15 0.43
20 2 0.06
21 7 0.20
22 11 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTAAAATTAATTTT
Found at i:957262 original size:27 final size:28
Alignment explanation
Indices: 957232--957289 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
957222 TTTTTAAATT
*
957232 ATTATTAAA-CAT-GATAATTTAATAAAA
1 ATTATTAAATCATCAATAATTTAA-AAAA
*
957259 ATTATTAAATCATCAATAATTTTAAAAA
1 ATTATTAAATCATCAATAATTTAAAAAA
957287 ATT
1 ATT
957290 TTCTCGTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 10 0.37
29 8 0.30
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTATTAAATCATCAATAATTTAAAAAA
Found at i:959453 original size:517 final size:517
Alignment explanation
Indices: 958480--959512 Score: 1796
Period size: 517 Copynumber: 2.0 Consensus size: 517
958470 CTCATAACTT
*
958480 TAAGTGTGTCATTCCCTGTACAAACATAGCCATAGCTTGGTCACTTCGATTGTTCTCTTAGGCCA
1 TAAGTGTGTCATTCCCTGCACAAACATAGCCATAGCTTGGTCACTTCGATTGTTCTCTTAGGCCA
958545 TGAGAAGCAAAAATGTCCTCTTTTTAATGGTAATCCACACAAATGATTAGTGAAGACTTCTTAAA
66 TGAGAAGCAAAAATGTCCTCTTTTTAATGGTAATCCACACAAATGATTAGTGAAGACTTCTTAAA
* * *
958610 GCATAATAATTCACCCATACTAGCGGGCTGCTATTAGATTTACTATTGTCAGGACGTACGCTCAC
131 GCATAATAATTCACCCATACTAGCGGGCTGCTATCAGATTTACTATTGTCAAGACATACGCTCAC
* * * *
958675 CCCGATGATAAGAAAAATGAGGCGTGCCCCACTTAATATCTTTTGCGATTAGGGATTTCTATGGT
196 CCCGATGATAAAAAAAATGAGACGTGCCCCACTTAATATCCTTCGCGATTAGGGATTTCTATGGT
* * * *
958740 GTGATAGGAAATGTGTATTGATTGAAGTAGGGAAGATAGGTCGATAAATTGCCCATCTAACTGAT
261 GTGATAGGAAATGCGTATTGATTGAAGTAGAGAAGATAGGTCGATAAATTGCCCATCCAACCGAT
*
958805 CCTCAACAGTCACTACAAGTGGTCAAAGTTTTGGAGTCGGCACCAATTATTTCAGGCGTGATATG
326 CCTCAACAGTCACTACAAGTGGTCAAAGTTTTGGAGTCGCCACCAATTATTTCAGGCGTGATATG
* *
958870 ATTAGATACCTATTGAAACCTATGTTTTGAGTTACGAAACTTGAAACATCGATTTCGTGGTCTAC
391 ATTAGATACCTATTGAAACCTATGTTTTAAGTTACGAAACTTGAAACATCGATCTCGTGGTCTAC
* *
958935 GTAATTCAAAGATTCGTCGATTGACTTCGAGAGTTGGTTATGTACAAAGAGGTATAAACCTC
456 GTAATTCAAAGATTCATCGATTGACTTCGAGAGTTGGTTACGTACAAAGAGGTATAAACCTC
958997 TAAGTGTGTCATTCCCTGCACAAACATAGCCATAGCTTGGTCACTTCGATTGTTCTCTTAGGCCA
1 TAAGTGTGTCATTCCCTGCACAAACATAGCCATAGCTTGGTCACTTCGATTGTTCTCTTAGGCCA
959062 TGAGAAGCAAAAATGTCCTCTTTTTAATGGTAATCCACACAAATGATTAGTGAAGACTTCTTAAA
66 TGAGAAGCAAAAATGTCCTCTTTTTAATGGTAATCCACACAAATGATTAGTGAAGACTTCTTAAA
* *
959127 GCATAATAATTCACCCATACTAGCGGGCTGTTATCAGATTTACTATTGTCAAGACATACGCTCGC
131 GCATAATAATTCACCCATACTAGCGGGCTGCTATCAGATTTACTATTGTCAAGACATACGCTCAC
* *
959192 CCCGTTGATAAAAAAAATGAGACGTGCCCCACTTAATATCCTTCGTGATTAGGGATTTCTATGGT
196 CCCGATGATAAAAAAAATGAGACGTGCCCCACTTAATATCCTTCGCGATTAGGGATTTCTATGGT
*
959257 GTGATAGGAAATGCGTATTGATTGAAGTAGAGAAGATCGGTCGATAAATTGCCCATCCAACCGAT
261 GTGATAGGAAATGCGTATTGATTGAAGTAGAGAAGATAGGTCGATAAATTGCCCATCCAACCGAT
* * *
959322 CCTCAACGGTCACTACAAGTGGTCAAAGTTTTGGAGTCGCCACCGATTATTTCGGGCGTGATATG
326 CCTCAACAGTCACTACAAGTGGTCAAAGTTTTGGAGTCGCCACCAATTATTTCAGGCGTGATATG
* **
959387 ATTAGATGCCTATTGAAATTTATGTTTTAAGTTACGAAACTTGAAACATCGATCTCGTGGTCTAC
391 ATTAGATACCTATTGAAACCTATGTTTTAAGTTACGAAACTTGAAACATCGATCTCGTGGTCTAC
* *
959452 GTAATTCAAAGATTCATCGATTGACTTCGGGAGTTGGTTACGTGCAAAGAGGTATAAACCT
456 GTAATTCAAAGATTCATCGATTGACTTCGAGAGTTGGTTACGTACAAAGAGGTATAAACCT
959513 TTTTGTGATG
Statistics
Matches: 486, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
517 486 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (517 bp):
TAAGTGTGTCATTCCCTGCACAAACATAGCCATAGCTTGGTCACTTCGATTGTTCTCTTAGGCCA
TGAGAAGCAAAAATGTCCTCTTTTTAATGGTAATCCACACAAATGATTAGTGAAGACTTCTTAAA
GCATAATAATTCACCCATACTAGCGGGCTGCTATCAGATTTACTATTGTCAAGACATACGCTCAC
CCCGATGATAAAAAAAATGAGACGTGCCCCACTTAATATCCTTCGCGATTAGGGATTTCTATGGT
GTGATAGGAAATGCGTATTGATTGAAGTAGAGAAGATAGGTCGATAAATTGCCCATCCAACCGAT
CCTCAACAGTCACTACAAGTGGTCAAAGTTTTGGAGTCGCCACCAATTATTTCAGGCGTGATATG
ATTAGATACCTATTGAAACCTATGTTTTAAGTTACGAAACTTGAAACATCGATCTCGTGGTCTAC
GTAATTCAAAGATTCATCGATTGACTTCGAGAGTTGGTTACGTACAAAGAGGTATAAACCTC
Found at i:965290 original size:12 final size:12
Alignment explanation
Indices: 965273--965297 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
965263 GGAGCCACAT
965273 TTTCCATCCATA
1 TTTCCATCCATA
965285 TTTCCATCCATA
1 TTTCCATCCATA
965297 T
1 T
965298 CTCAACCAAA
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTCCATCCATA
Found at i:971046 original size:51 final size:50
Alignment explanation
Indices: 970988--971224 Score: 280
Period size: 51 Copynumber: 4.9 Consensus size: 50
970978 TTTTAACTAG
*
970988 ATGTATCGATACATTGAATAATGTATAGATACATCTGGGTAAAAAGACAAA
1 ATGTATCGATACATTGAA-AATGTATCGATACATCTGGGTAAAAAGACAAA
* *
971039 ATGTATCGATACATTGAAGAATGTATCGATACA--T---T---CATAC---
1 ATGTATCGATACATTGAA-AATGTATCGATACATCTGGGTAAAAAGACAAA
* * *
971079 ATGTATCGATACATTGAAAACTATATCGATACATCTGGGTAAAAAAACATA
1 ATGTATCGATACATTGAAAA-TGTATCGATACATCTGGGTAAAAAGACAAA
*
971130 ATGTATCGATACATTGAAAACTGTATCGATACATCTGGGTAAAAAGATAAA
1 ATGTATCGATACATTGAAAA-TGTATCGATACATCTGGGTAAAAAGACAAA
*
971181 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGGTAAAA
1 ATGTATCGATACATTGAA-AATGTATCGATACATCTGGGTAAAA
971225 TAGGACTTTT
Statistics
Matches: 161, Mismatches: 12, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
39 2 0.01
40 29 0.18
42 1 0.01
43 3 0.02
45 1 0.01
46 1 0.01
48 3 0.02
49 1 0.01
51 118 0.73
52 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAATGTATCGATACATCTGGGTAAAAAGACAAA
Found at i:971063 original size:20 final size:19
Alignment explanation
Indices: 971036--971112 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
971026 GTAAAAAGAC
971036 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
971055 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
*
971075 ATACATGTATCGATACATTG
1 A-AAATGTATCGATACATTG
*
971095 AAAACTATATCGATACAT
1 AAAA-TGTATCGATACAT
971113 CTGGGTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.08
20 45 0.90
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:971143 original size:91 final size:91
Alignment explanation
Indices: 970988--971163 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 91
970978 TTTTAACTAG
* *
970988 ATGTATCGATACATTGAATAATGTATAGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTGAATAATATATAGATACATCTGGGTAAAAAAACAAAATGTATCGATACAT
971053 TGAAGAA-TGTATCGATACATTCATAC
66 TGAA-AACTGTATCGATACATTCATAC
* *
971079 ATGTATCGATACATTGAA-AACTATATCGATACATCTGGGTAAAAAAACATAATGTATCGATACA
1 ATGTATCGATACATTGAATAA-TATATAGATACATCTGGGTAAAAAAACAAAATGTATCGATACA
971143 TTGAAAACTGTATCGATACAT
65 TTGAAAACTGTATCGATACAT
971164 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
90 4 0.05
91 75 0.95
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (91 bp):
ATGTATCGATACATTGAATAATATATAGATACATCTGGGTAAAAAAACAAAATGTATCGATACAT
TGAAAACTGTATCGATACATTCATAC
Found at i:971173 original size:24 final size:20
Alignment explanation
Indices: 971036--971163 Score: 91
Period size: 20 Copynumber: 5.9 Consensus size: 20
971026 GTAAAAAGAC
971036 AAAA-TGTATCGATACATTG
1 AAAACTGTATCGATACATTG
971055 AAGAA-TGTATCGATACATT-
1 AA-AACTGTATCGATACATTG
* *
971074 CATACATGTATCGATACATTG
1 AAAAC-TGTATCGATACATTG
*
971095 AAAACTATATCGATACATCTGGG
1 AAAACTGTATCGATACAT-T--G
971118 TAAAAAAACATAATGTATCGATACATTG
1 ----AAAAC----TGTATCGATACATTG
971146 AAAACTGTATCGATACAT
1 AAAACTGTATCGATACAT
971164 CTGGGTAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 29
0.72 0.05 0.24
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 55 0.62
21 4 0.05
23 1 0.01
24 5 0.06
27 5 0.06
28 1 0.01
30 1 0.01
31 12 0.14
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAACTGTATCGATACATTG
Found at i:972138 original size:13 final size:13
Alignment explanation
Indices: 972120--972149 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
972110 GATACATGCG
972120 ACATTATATCAAT
1 ACATTATATCAAT
*
972133 ACATTATATCGAT
1 ACATTATATCAAT
972146 ACAT
1 ACAT
972150 AGTGAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (13 bp):
ACATTATATCAAT
Found at i:978310 original size:13 final size:13
Alignment explanation
Indices: 978292--978316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
978282 AAAACCCAGA
978292 TGTATTGATACAT
1 TGTATTGATACAT
978305 TGTATTGATACA
1 TGTATTGATACA
978317 AGGGCACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:980196 original size:21 final size:21
Alignment explanation
Indices: 980172--980211 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
980162 TTTGAAATAG
980172 GGAGAGATTATTATGGAAAAA
1 GGAGAGATTATTATGGAAAAA
*
980193 GGAGAGATTATTTTGGAAA
1 GGAGAGATTATTATGGAAA
980212 CAAAAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (21 bp):
GGAGAGATTATTATGGAAAAA
Found at i:980234 original size:28 final size:27
Alignment explanation
Indices: 980193--980246 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
980183 TATGGAAAAA
*
980193 GGAGAGATTATTTTGGAAACAAA-AAGGG
1 GGAGAAATTATTTT--AAACAAAGAAGGG
*
980221 GGAGAAATTTTTTTAAACAAAGAAGG
1 GGAGAAATTATTTTAAACAAAGAAGG
980247 AGTTATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 12 0.52
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.24
Consensus pattern (27 bp):
GGAGAAATTATTTTAAACAAAGAAGGG
Found at i:981030 original size:61 final size:62
Alignment explanation
Indices: 980954--981108 Score: 224
Period size: 61 Copynumber: 2.5 Consensus size: 62
980944 TACAACTATT
*
980954 TGTATCGATACATAGTGAAAAGTATCGATACATTGTGCCCAATGAC-TAAATTTCAAATGCA
1 TGTATCGATACATAGTGAAAAGTATCGATACATTGTGCCCAACGACATAAATTTCAAATGCA
* * * * *
981015 TGTATCGATATATAGTAAAAAATATTGATACATTGTGCCCAACGGCTATAAATTTCAAATGCA
1 TGTATCGATACATAGTGAAAAGTATCGATACATTGTGCCCAACGAC-ATAAATTTCAAATGCA
981078 TGTATCGATACATTA-TGAAAAGTATCGATAC
1 TGTATCGATACA-TAGTGAAAAGTATCGATAC
981109 GTAATATCGG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
61 40 0.49
63 39 0.48
64 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (62 bp):
TGTATCGATACATAGTGAAAAGTATCGATACATTGTGCCCAACGACATAAATTTCAAATGCA
Found at i:983431 original size:20 final size:20
Alignment explanation
Indices: 983397--983446 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
983387 TAACTGGATG
* *
983397 TATCGATATATTGAAGAATA
1 TATCGATACAATGAAGAATA
* *
983417 TATCTATACAATGAAGAATG
1 TATCGATACAATGAAGAATA
983437 TATCGATACA
1 TATCGATACA
983447 TTTAGATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (20 bp):
TATCGATACAATGAAGAATA
Found at i:985939 original size:198 final size:198
Alignment explanation
Indices: 985601--985998 Score: 796
Period size: 198 Copynumber: 2.0 Consensus size: 198
985591 AATTAAGGTT
985601 AATAAAACCTATATAGTTTATCTCAATCTCTAATACTAAAATATCTTATAAATAGCCAAAAACTT
1 AATAAAACCTATATAGTTTATCTCAATCTCTAATACTAAAATATCTTATAAATAGCCAAAAACTT
985666 GAAAAAGAAAAACTTGGCATATGTCACGACGCGCTCAACCCCCGACGATAGGGCAAATGAGGCGC
66 GAAAAAGAAAAACTTGGCATATGTCACGACGCGCTCAACCCCCGACGATAGGGCAAATGAGGCGC
985731 GCCCGACTTAATATCCCTCGTAATTGGGGATTTCTATGGCATGATAAAAGGTATATTCATTGAAG
131 GCCCGACTTAATATCCCTCGTAATTGGGGATTTCTATGGCATGATAAAAGGTATATTCATTGAAG
985796 GGG
196 GGG
985799 AATAAAACCTATATAGTTTATCTCAATCTCTAATACTAAAATATCTTATAAATAGCCAAAAACTT
1 AATAAAACCTATATAGTTTATCTCAATCTCTAATACTAAAATATCTTATAAATAGCCAAAAACTT
985864 GAAAAAGAAAAACTTGGCATATGTCACGACGCGCTCAACCCCCGACGATAGGGCAAATGAGGCGC
66 GAAAAAGAAAAACTTGGCATATGTCACGACGCGCTCAACCCCCGACGATAGGGCAAATGAGGCGC
985929 GCCCGACTTAATATCCCTCGTAATTGGGGATTTCTATGGCATGATAAAAGGTATATTCATTGAAG
131 GCCCGACTTAATATCCCTCGTAATTGGGGATTTCTATGGCATGATAAAAGGTATATTCATTGAAG
985994 GGG
196 GGG
985997 AA
1 AA
985999 GATCAGTAGG
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 200 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (198 bp):
AATAAAACCTATATAGTTTATCTCAATCTCTAATACTAAAATATCTTATAAATAGCCAAAAACTT
GAAAAAGAAAAACTTGGCATATGTCACGACGCGCTCAACCCCCGACGATAGGGCAAATGAGGCGC
GCCCGACTTAATATCCCTCGTAATTGGGGATTTCTATGGCATGATAAAAGGTATATTCATTGAAG
GGG
Found at i:989314 original size:13 final size:13
Alignment explanation
Indices: 989296--989353 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
989286 ACATTTGGTC
989296 ATGTATCGATACA
1 ATGTATCGATACA
989309 ATGTATCGATACA
1 ATGTATCGATACA
989322 TCTTGTATGTATCGATACA
1 ------ATGTATCGATACA
989341 ATGTATCGATACA
1 ATGTATCGATACA
989354 TCTTGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 26 0.67
19 13 0.33
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:989333 original size:19 final size:19
Alignment explanation
Indices: 989309--989372 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
989299 TATCGATACA
989309 ATGTATCGATACATCTTGT
1 ATGTATCGATACATCTTGT
989328 ATGTATCGATACA------
1 ATGTATCGATACATCTTGT
989341 ATGTATCGATACATCTTGT
1 ATGTATCGATACATCTTGT
989360 ATGTATCGATACA
1 ATGTATCGATACA
989373 AACAGTTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 13 0.33
19 26 0.67
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATCTTGT
Found at i:989337 original size:32 final size:32
Alignment explanation
Indices: 989274--989373 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
989264 CGTTACAAGC
989274 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
989307 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
989339 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
989371 CAA
1 CAA
989374 ACAGTTAAGG
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
32 46 0.70
33 18 0.27
34 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:989472 original size:13 final size:13
Alignment explanation
Indices: 989454--989478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
989444 ACATTTGGTC
989454 ATGTATCAATACA
1 ATGTATCAATACA
989467 ATGTATCAATAC
1 ATGTATCAATAC
989479 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:990040 original size:21 final size:22
Alignment explanation
Indices: 990014--990081 Score: 93
Period size: 24 Copynumber: 3.0 Consensus size: 22
990004 TTTCCTTTTC
990014 TCTCCCCCTTAATAAAA-AATT
1 TCTCCCCCTTAATAAAAGAATT
*
990035 TCTCCCCCTTAATAAAAGATTTT
1 TCTCCCCCTTAATAAAAGA-ATT
*
990058 CTCTCCCCCTTAATAAAATAATT
1 -TCTCCCCCTTAATAAAAGAATT
990081 T
1 T
990082 TCTTTAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 17 0.41
22 2 0.05
23 4 0.10
24 18 0.44
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAAGAATT
Found at i:990067 original size:24 final size:23
Alignment explanation
Indices: 990009--990084 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 23
989999 TTCATTTTCC
990009 TTTTCTCTCCCCCTTAATAAAAA
1 TTTTCTCTCCCCCTTAATAAAAA
*
990032 -ATT-TCTCCCCCTTAATAAAAGA
1 TTTTCTCTCCCCCTTAATAAAA-A
990054 TTTTCTCTCCCCCTTAATAAAATAA
1 TTTTCTCTCCCCCTTAAT-AAA-AA
990079 TTTTCT
1 TTTTCT
990085 TTAATCACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 17 0.37
22 3 0.07
23 2 0.04
24 13 0.28
25 10 0.22
26 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.01, T:0.41
Consensus pattern (23 bp):
TTTTCTCTCCCCCTTAATAAAAA
Found at i:998170 original size:13 final size:13
Alignment explanation
Indices: 998152--998177 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
998142 ACATTTGGTC
998152 ATGTATCGATACA
1 ATGTATCGATACA
998165 ATGTATCGATACA
1 ATGTATCGATACA
998178 TCTTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:998173 original size:33 final size:32
Alignment explanation
Indices: 998131--998197 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
998121 GTTACAAGCT
998131 AATGTATCGATACAT-TTGGTCATGTATCGATAC
1 AATGTATCGATACATCTT-GT-ATGTATCGATAC
*
998164 AATGTATCGATACATCTTGTGTGTATCGATAC
1 AATGTATCGATACATCTTGTATGTATCGATAC
998196 AA
1 AA
998198 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.41
33 17 0.53
34 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATCTTGTATGTATCGATAC
Found at i:998227 original size:11 final size:11
Alignment explanation
Indices: 998211--998243 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
998201 GTTAAGGGTG
*
998211 GCTACTACCAA
1 GCTACTGCCAA
998222 GCTACTGCCAA
1 GCTACTGCCAA
998233 GCTACTGCCAA
1 GCTACTGCCAA
998244 TCACCTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.36, G:0.15, T:0.18
Consensus pattern (11 bp):
GCTACTGCCAA
Found at i:998307 original size:13 final size:13
Alignment explanation
Indices: 998289--998313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
998279 ACATTTGGTC
998289 ATGTATTGATACA
1 ATGTATTGATACA
998302 ATGTATTGATAC
1 ATGTATTGATAC
998314 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:999188 original size:20 final size:20
Alignment explanation
Indices: 999162--999216 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
999152 AAAAAGACAG
*
999162 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
999182 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
999202 AATGTATCGATACAT
1 AATGTATCGATACAT
999217 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1005179 original size:32 final size:33
Alignment explanation
Indices: 1005138--1005206 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
1005128 AAAGCTTTGA
* * *
1005138 AAAATGACATTTGTTTTTGATACTGTTAAATT-
1 AAAACGACATTTATTTTTGATACTATTAAATTC
* *
1005170 AAAACGACATTTATTTTTTATATTATTAAATTC
1 AAAACGACATTTATTTTTGATACTATTAAATTC
1005203 AAAA
1 AAAA
1005207 TAAAAAAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 27 0.87
33 4 0.13
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (33 bp):
AAAACGACATTTATTTTTGATACTATTAAATTC
Found at i:1005977 original size:23 final size:23
Alignment explanation
Indices: 1005943--1005989 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1005933 GAAATGTACA
1005943 TATGTATCTTTTGGCTCTTAATC
1 TATGTATCTTTTGGCTCTTAATC
* * *
1005966 TATGTATTTTTTTGTTCTTAATC
1 TATGTATCTTTTGGCTCTTAATC
1005989 T
1 T
1005990 GACTCACCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.60
Consensus pattern (23 bp):
TATGTATCTTTTGGCTCTTAATC
Found at i:1009163 original size:34 final size:35
Alignment explanation
Indices: 1009116--1009201 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
1009106 TGACTTTATG
1009116 TTATT-AATCATATTATTTAATTTAATACATA-TTA
1 TTATTAAATCATATT-TTTAATTTAATACATATTTA
* *
1009150 TTATTAAAT-ATATTTTTTATTTAATACTTATTTA
1 TTATTAAATCATATTTTTAATTTAATACATATTTA
*
1009184 CTATTAAATTACATATTT
1 TTATTAAA-T-CATATTT
1009202 AACTGTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 14 0.32
34 20 0.45
35 4 0.09
37 6 0.14
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATTAAATCATATTTTTAATTTAATACATATTTA
Found at i:1010698 original size:13 final size:13
Alignment explanation
Indices: 1010680--1010705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1010670 CAATTTTTGG
1010680 TGTATCGATACAT
1 TGTATCGATACAT
1010693 TGTATCGATACAT
1 TGTATCGATACAT
1010706 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1010717 original size:32 final size:33
Alignment explanation
Indices: 1010660--1010723 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1010650 TACAAGCCAA
**
1010660 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1010693 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1010724 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1010730 original size:19 final size:18
Alignment explanation
Indices: 1010660--1010730 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1010650 TACAAGCCAA
1010660 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1010680 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1010693 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1010712 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1010731 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1013272 original size:13 final size:13
Alignment explanation
Indices: 1013254--1013292 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1013244 ATAATTACCC
*
1013254 TGTATCGATACAT
1 TGTATCGATACAA
1013267 TGTATCGATACAA
1 TGTATCGATACAA
1013280 TGTATCGATACAA
1 TGTATCGATACAA
1013293 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1017226 original size:21 final size:23
Alignment explanation
Indices: 1017200--1017248 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1017190 ATGCAAGTTT
1017200 TTATTTTTC-TTAGCCAAC-TCA
1 TTATTTTTCATTAGCCAACTTCA
*
1017221 TTA-TTTTCATTAGCCAACTTCT
1 TTATTTTTCATTAGCCAACTTCA
1017243 TTATTT
1 TTATTT
1017249 CAACTTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 12 0.50
22 5 0.21
23 2 0.08
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (23 bp):
TTATTTTTCATTAGCCAACTTCA
Found at i:1019475 original size:13 final size:13
Alignment explanation
Indices: 1019457--1019482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1019447 CAATTTTTGG
1019457 TGTATCGATACAT
1 TGTATCGATACAT
1019470 TGTATCGATACAT
1 TGTATCGATACAT
1019483 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1019494 original size:32 final size:33
Alignment explanation
Indices: 1019437--1019500 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1019427 TACAAGCCAA
**
1019437 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1019470 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1019501 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1019507 original size:19 final size:18
Alignment explanation
Indices: 1019437--1019507 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1019427 TACAAGCCAA
1019437 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1019457 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1019470 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1019489 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1019508 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1024260 original size:52 final size:52
Alignment explanation
Indices: 1024175--1024299 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1024165 ATATGAAAAG
* *
1024175 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1024227 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1024279 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1024300 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1024312 original size:52 final size:51
Alignment explanation
Indices: 1024175--1024319 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
1024165 ATATGAAAAG
*
1024175 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1024227 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1024279 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1024320 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1024326 original size:13 final size:13
Alignment explanation
Indices: 1024308--1024332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1024298 CAAAGATCAG
1024308 TGTATCGATACAA
1 TGTATCGATACAA
1024321 TGTATCGATACA
1 TGTATCGATACA
1024333 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1024414 original size:33 final size:33
Alignment explanation
Indices: 1024372--1024441 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1024362 GGCAGTAGCT
1024372 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1024405 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1024438 TACA
1 TACA
1024442 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1024415 original size:13 final size:13
Alignment explanation
Indices: 1024397--1024421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1024387 CAAAAAAATA
1024397 TGTATCGATACAT
1 TGTATCGATACAT
1024410 TGTATCGATACA
1 TGTATCGATACA
1024422 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1028408 original size:15 final size:15
Alignment explanation
Indices: 1028388--1028417 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1028378 GCTTACCATC
*
1028388 ATTTCCATTTTCAAA
1 ATTTCCATTATCAAA
1028403 ATTTCCATTATCAAA
1 ATTTCCATTATCAAA
1028418 TGAATCCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTCCATTATCAAA
Found at i:1033659 original size:15 final size:15
Alignment explanation
Indices: 1033639--1033668 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1033629 ATGGTAACAT
1033639 GTTAGGACCACTAAA
1 GTTAGGACCACTAAA
1033654 GTTAGGACCACTAAA
1 GTTAGGACCACTAAA
1033669 ATGATGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
GTTAGGACCACTAAA
Found at i:1035458 original size:61 final size:62
Alignment explanation
Indices: 1035292--1035573 Score: 200
Period size: 61 Copynumber: 4.8 Consensus size: 62
1035282 AATGAGAAAA
* ** * * * * *
1035292 GTGCCAATATGCTGATTCGAGGTTAGCGATATTAGACTTAAGGATG-TGAAGAATGATAGAA-
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGAAGAAAGATA-AAG
* * * ** * *
1035353 GTGTCGATATGCTGATTCATA-ACC-GACGATATCAGGCCTGAAGATGAAG-AGAAAGATAAAG
1 GTGCCAATATGCTGATTCA-AGGCCAG-CGATATTGGGCTTAAAGATGAAGAAGAAAGATAAAG
*
1035414 GTGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGAT------G--A-A-AAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGAAGAAAGATAAAG
* * * * * *
1035466 GTGCCAATGTGCTGATTTAAGGCCAACAACATTGGGCTTAAAGAT-AAGAAGAATGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGAAGAAAGATAAAG
* * *
1035527 GTGCCGATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGATGA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGA
1035574 CAAAGGCACC
Statistics
Matches: 169, Mismatches: 36, Indels: 31
0.72 0.15 0.13
Matches are distributed among these distances:
52 43 0.25
53 1 0.01
54 1 0.01
56 1 0.01
57 1 0.01
60 5 0.03
61 113 0.67
62 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (62 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGAAGAAAGATAAAG
Found at i:1035479 original size:52 final size:52
Alignment explanation
Indices: 1035410--1035672 Score: 231
Period size: 52 Copynumber: 4.9 Consensus size: 52
1035400 AGAGAAAGAT
* *
1035410 AAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA
* * * * * *
1035462 AAAGGTGCCAATGTGCTGATTTAAGGCCAACAACATTGGGCTTAAAGATAAGAAGAATGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-----G-A--A
* * *
1035522 TAAAGGTGCCGATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGATGAC
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA
** * * * *
1035575 AAAGGCACCAATATGCTAATTCAAGGCCAACGATATTAGACTT-AAGAAAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-ATGAA
** * * *
1035627 AAAGGTGCCAAGGTGCTAATTCCAGGCCAGCGACATTGGACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1035673 AAAAAGATGG
Statistics
Matches: 168, Mismatches: 32, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
51 3 0.02
52 117 0.70
53 2 0.01
55 1 0.01
56 1 0.01
57 1 0.01
58 1 0.01
60 1 0.01
61 41 0.24
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA
Found at i:1035560 original size:113 final size:113
Alignment explanation
Indices: 1035393--1035605 Score: 311
Period size: 113 Copynumber: 1.9 Consensus size: 113
1035383 ATCAGGCCTG
* * *
1035393 AAGATGAAGAGAAAGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGA
1 AAGATGAAGAGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGA
** * * *
1035458 TGAAAAAGGTGCCAATGTGCTGATTTAAGGCCAACAACATTGGGCTTA
66 TGAAAAAGGCACCAATATGCTAATTCAAGGCCAACAACATTGGGCTTA
* *
1035506 AAGAT-AAGAAGAATGATAAAGGTGCCGATATGCTGATACAAGGCCAGCGATATTGGACTTAAAG
1 AAGATGAAG-AGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAG
*
1035570 ATGACAAAGGCACCAATATGCTAATTCAAGGCCAAC
65 ATGAAAAAGGCACCAATATGCTAATTCAAGGCCAAC
1035606 GATATTAGAC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 3 0.03
113 85 0.97
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (113 bp):
AAGATGAAGAGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGA
TGAAAAAGGCACCAATATGCTAATTCAAGGCCAACAACATTGGGCTTA
Found at i:1035619 original size:113 final size:112
Alignment explanation
Indices: 1035393--1035630 Score: 302
Period size: 113 Copynumber: 2.1 Consensus size: 112
1035383 ATCAGGCCTG
* * *
1035393 AAGATGAAG-AGAAAGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAG
1 AAGAT-AAGAAGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAG
** * * * * *
1035457 ATGAAAAAGGTGCCAATGTGCTGATTTAAGGCCAACAACATTGGGCTT
65 ATGAAAAAGGCACCAATATGCTAATTCAAGGCCAACAACATTAGACTT
* *
1035505 AAAGATAAGAAGAATGATAAAGGTGCCGATATGCTGATACAAGGCCAGCGATATTGGACTTAAAG
1 -AAGATAAGAAGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAG
* * *
1035570 ATGACAAAGGCACCAATATGCTAATTCAAGGCCAACGATATTAGACTT
65 ATGAAAAAGGCACCAATATGCTAATTCAAGGCCAACAACATTAGACTT
1035618 AAGA-AAGAA-AAAG
1 AAGATAAGAAGAAAG
1035631 GTGCCAAGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
110 3 0.03
111 5 0.05
112 7 0.06
113 93 0.86
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (112 bp):
AAGATAAGAAGAAAGATAAAGGTGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGA
TGAAAAAGGCACCAATATGCTAATTCAAGGCCAACAACATTAGACTT
Found at i:1035915 original size:32 final size:32
Alignment explanation
Indices: 1035746--1036171 Score: 270
Period size: 32 Copynumber: 12.9 Consensus size: 32
1035736 ATGCCATCGA
* *
1035746 CTTGTGTGGGCTTTTG-AGAGGGTTGCTACC-G
1 CTTGTGTGGGC-TTTGAAGAAGGTTGCCACCAG
* * * * *
1035777 ACTTATGTAGGCTTTGGAA-AGGGTTTCCACCAA
1 -CTTGTGTGGGCTTT-GAAGAAGGTTGCCACCAG
* * *
1035810 CTTATGTGGGCTTTAAAGAAGGTTGCCACTAG
1 CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
* * * *
1035842 CTTATGTGGGCTTTTGAAGGGAAATGTTGCCACTAA
1 CTTGTGTGGGC-TTTGAA--G-AAGGTTGCCACCAG
1035878 CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
1 CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
* * * * *
1035910 TTTGTGTGGGCTTCGAAAAAGGTTGCCACTAA
1 CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
* * * *
1035942 CTTATATGGGCTTTTAAGAGGAAAAGGTTACCACC-G
1 CTTGTGTGGGC-TTT--GA--AGAAGGTTGCCACCAG
* *
1035978 ACTTGTGTGAGCTTTGAAGAAGGTTGCCATCAG
1 -CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
* *
1036011 CTTGTGTGAGCTTTGGAA-AACGTTGCCACCAG
1 CTTGTGTGGGCTTT-GAAGAAGGTTGCCACCAG
* * * *
1036043 CTTGTGTGGGTTTTCAAGGGAGAGGCTACCACC-G
1 CTTGTGTGGGCTTTGAA--GA-AGGTTGCCACCAG
* * *
1036077 ACTTGTGTGAGCTTTGAAGAAAGTTGCAACCAG
1 -CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
* * * *
1036110 CTTGTGTGGGCTTTGGAGATGGGTTGCCACTAA
1 CTTGTGTGGGCTTTGAAGA-AGGTTGCCACCAG
* *
1036143 CTTGTGTGAGCTTTGGAGATAGGTTGCCA
1 CTTGTGTGGGCTTTGAAGA-AGGTTGCCA
1036172 TTGACTTATG
Statistics
Matches: 311, Mismatches: 60, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
31 7 0.02
32 173 0.56
33 51 0.16
34 4 0.01
35 31 0.10
36 25 0.08
37 20 0.06
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (32 bp):
CTTGTGTGGGCTTTGAAGAAGGTTGCCACCAG
Found at i:1036036 original size:101 final size:100
Alignment explanation
Indices: 1035773--1036156 Score: 400
Period size: 100 Copynumber: 3.8 Consensus size: 100
1035763 GAGGGTTGCT
* * * * * *
1035773 ACCGACTTATGT-AGGCTTTGGAA-AGGGTTTCCACCAACTTATGTGGGCTTT-AAAGAAGGTTG
1 ACCGACTTGTGTGA-GCTTT-GAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAA-AAGGTTG
* * * *
1035835 CCACTAGCTTATGTGGGCTTTTGAAGGGAAATGTTGCC
63 CCACTAACTTATGTGGGCTTTTCAAGGGAAAGGTTACC
** * * * *
1035873 ACTAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGTTTGTGTGGGCTTCGAAAAAGGTTGCCA
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAAGGTTGCCA
*
1035938 CTAACTTATATGGGCTTTT-AAGAGGAAAAGGTTACC
66 CTAACTTATGTGGGCTTTTCAAG-GG-AAAGGTTACC
* * *
1035974 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCATCAGCTTGTGTGAGCTTTGGAAAACGTTGCCA
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAAGGTTGCCA
* * * * *
1036039 CCAGCTTGTGTGGG-TTTTCAAGGGAGAGGCTACC
66 CTAACTTATGTGGGCTTTTCAAGGGAAAGGTTACC
* * **
1036073 ACCGACTTGTGTGAGCTTTGAAGAAAGTTGCAACCAGCTTGTGTGGGCTTTGGAGATGGGTTGCC
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGA-AAAGGTTGCC
* *
1036138 ACTAACTTGTGTGAGCTTT
65 ACTAACTTATGTGGGCTTT
1036157 GGAGATAGGT
Statistics
Matches: 237, Mismatches: 39, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
99 64 0.27
100 90 0.38
101 83 0.35
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (100 bp):
ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAAGGTTGCCA
CTAACTTATGTGGGCTTTTCAAGGGAAAGGTTACC
Found at i:1036103 original size:99 final size:99
Alignment explanation
Indices: 1035773--1036126 Score: 383
Period size: 101 Copynumber: 3.5 Consensus size: 99
1035763 GAGGGTTGCT
* * * * * * *
1035773 ACCGACTTATGT-AGGCTTTGGAA-AGGGTTTCCACCAACTTATGTGGGCTTT-AAAGAAGGTTG
1 ACCGACTTGTGTGA-GCTTT-GAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAA-AACGTTG
* *
1035835 CCACTAGCTTATGTGGGCTTTTGAAGGGAAATGTTGCC
63 CCACTAGCTTATGTGGGCTTTT-AAGGGAAAGGTTACC
** * * * * *
1035873 ACTAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGTTTGTGTGGGCTTCGAAAAAGGTTGCCA
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAACGTTGCCA
* *
1035938 CTAACTTATATGGGCTTTTAAGAGGAAAAGGTTACC
66 CTAGCTTATGTGGGCTTTTAAG-GG-AAAGGTTACC
* *
1035974 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCATCAGCTTGTGTGAGCTTTGGAAAACGTTGCCA
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAACGTTGCCA
* * * *
1036039 CCAGCTTGTGTGGG-TTTTCAAGGGAGAGGCTACC
66 CTAGCTTATGTGGGCTTTT-AAGGGAAAGGTTACC
* *
1036073 ACCGACTTGTGTGAGCTTTGAAGAAAGTTGCAACCAGCTTGTGTGGGCTTTGGA
1 ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGA
1036127 GATGGGTTGC
Statistics
Matches: 215, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
99 64 0.30
100 71 0.33
101 80 0.37
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (99 bp):
ACCGACTTGTGTGAGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGGAAAACGTTGCCA
CTAGCTTATGTGGGCTTTTAAGGGAAAGGTTACC
Found at i:1037848 original size:28 final size:28
Alignment explanation
Indices: 1037795--1037853 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1037785 TCTTCTCTAT
* * * *
1037795 TTTTGATTGATTTTTTTTATTTTTTTTC
1 TTTTGATTGATTTTTTCTACTCTTTTGC
1037823 TTTTGATTGATTTTTTGCT-CTCTTTTGC
1 TTTTGATTGATTTTTT-CTACTCTTTTGC
1037851 TTT
1 TTT
1037854 GTTTTTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.73
Consensus pattern (28 bp):
TTTTGATTGATTTTTTCTACTCTTTTGC
Found at i:1051866 original size:20 final size:20
Alignment explanation
Indices: 1051840--1051895 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1051830 CAAAAACCCA
1051840 AAATGTATCGATACAATGAAT
1 AAATGTATCGATACAAT-AAT
* *
1051861 -AATGTATCGATATAAATAGT
1 AAATGTATCGATA-CAATAAT
1051881 AAATGTATCGATACA
1 AAATGTATCGATACA
1051896 TTTATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACAATAAT
Found at i:1051887 original size:21 final size:19
Alignment explanation
Indices: 1051839--1051893 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
1051829 TCAAAAACCC
*
1051839 AAAATGTATCGATACAATG
1 AAAATGTATCGATAAAATG
1051858 AATAATGTATCGATATAAATAG
1 AA-AATGTATCGATA-AAAT-G
*
1051880 TAAATGTATCGATA
1 AAAATGTATCGATA
1051894 CATTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATAAAATG
Found at i:1057495 original size:2 final size:2
Alignment explanation
Indices: 1057488--1057525 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1057478 CTTTATTTTA
1057488 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
1057526 TGCAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1058486 original size:77 final size:77
Alignment explanation
Indices: 1058285--1058513 Score: 302
Period size: 77 Copynumber: 3.0 Consensus size: 77
1058275 TTTTTACTCA
* * * *
1058285 TTTAATAAAAA-TAATAATATTATATTTTACTATCATTACAACTATTAGTTATCAAATTACGTAA
1 TTTAATAAAAAGTAATATTATTATATTTTATTATCTTTA-AACTATTAGTTATCAAATTACTTAA
*
1058349 TTTTTTACT-CTT
65 TTTTTTAATACTT
* * *
1058361 TTTAATAAAAAAGTAATATTATTATATTTTTATTATATTGAATCTATTAGTTATCAAATTACTTA
1 TTTAAT-AAAAAGTAATATTATTATA-TTTTATTATCTTTAAACTATTAGTTATCAAATTACTTA
*
1058426 ATTTTTAAATAC-T
64 ATTTTTTAATACTT
* *
1058439 TTTAATAAAAAGTAATATTATTTTATTTTATTATCTTTAAACTTATTAATTATCAAATTACTTAA
1 TTTAATAAAAAGTAATATTATTATATTTTATTATCTTTAAAC-TATTAGTTATCAAATTACTTAA
1058504 TTTTTTAATA
65 TTTTTTAATA
1058514 AAAATAATAT
Statistics
Matches: 133, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
76 20 0.15
77 53 0.40
78 49 0.37
79 11 0.08
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (77 bp):
TTTAATAAAAAGTAATATTATTATATTTTATTATCTTTAAACTATTAGTTATCAAATTACTTAAT
TTTTTAATACTT
Found at i:1060256 original size:18 final size:20
Alignment explanation
Indices: 1060226--1060275 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1060216 TTTTAAACTC
*
1060226 ATAT-TTAAGTTAGTTA-T-
1 ATATATTAAGTTAGATATTA
*
1060243 ATATATTAATTTAGATATTA
1 ATATATTAAGTTAGATATTA
*
1060263 ATATATTATGTTA
1 ATATATTAAGTTA
1060276 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 1 0.04
20 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (20 bp):
ATATATTAAGTTAGATATTA
Found at i:1060455 original size:10 final size:10
Alignment explanation
Indices: 1060440--1060468 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1060430 AGAGATAAAA
1060440 TATATTTTTT
1 TATATTTTTT
1060450 TATATTTTTT
1 TATATTTTTT
1060460 TAT-TTTTTT
1 TATATTTTTT
1060469 ATGTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TATATTTTTT
Found at i:1060478 original size:18 final size:18
Alignment explanation
Indices: 1060442--1060478 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1060432 AGATAAAATA
*
1060442 TATTTTTTTATATTTTTT
1 TATTTTTTTATATTGTTT
*
1060460 TATTTTTTTATGTTGTTT
1 TATTTTTTTATATTGTTT
1060478 T
1 T
1060479 TTAACCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (18 bp):
TATTTTTTTATATTGTTT
Found at i:1061030 original size:20 final size:22
Alignment explanation
Indices: 1060978--1061019 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1060968 ATAATAGAGA
*
1060978 AATAATTTTTTTATTAAATATG
1 AATACTTTTTTTATTAAATATG
1061000 AATACTTTTTTGTA-TAAATA
1 AATACTTTTTT-TATTAAATA
1061020 GATAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
AATACTTTTTTTATTAAATATG
Found at i:1061705 original size:21 final size:23
Alignment explanation
Indices: 1061664--1061707 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1061654 TTGAATTCTG
1061664 TAAAAAAAATAATATATTAAATA
1 TAAAAAAAATAATATATTAAATA
*
1061687 TAAAAAAATTAATA-A-TAAATA
1 TAAAAAAAATAATATATTAAATA
1061708 ATTCTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
23 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAAAATAATATATTAAATA
Found at i:1062200 original size:26 final size:27
Alignment explanation
Indices: 1062159--1062213 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
1062149 TTAATTATAA
* *
1062159 AATATATAAATAATAATATATAATTTT
1 AATATATAAATAATAAAATAAAATTTT
1062186 AATA-ATAAATAATAAAATAAAATTTT
1 AATATATAAATAATAAAATAAAATTTT
1062212 AA
1 AA
1062214 ATCACTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATATATAAATAATAAAATAAAATTTT
Found at i:1064523 original size:15 final size:15
Alignment explanation
Indices: 1064503--1064533 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1064493 CACTTCACGA
1064503 CAAGTTTAACATGTG
1 CAAGTTTAACATGTG
1064518 CAAGTTTAACATGTG
1 CAAGTTTAACATGTG
1064533 C
1 C
1064534 TTACTATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (15 bp):
CAAGTTTAACATGTG
Found at i:1065514 original size:21 final size:22
Alignment explanation
Indices: 1065477--1065519 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1065467 TATCATAATA
*
1065477 TAAAAAATTTTGATATA-ATTT
1 TAAAAAATATTGATATATATTT
1065498 TAAAAAATATT-ATTATATATTT
1 TAAAAAATATTGA-TATATATTT
1065520 ATTTACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAAAATATTGATATATATTT
Found at i:1066921 original size:2 final size:2
Alignment explanation
Indices: 1066904--1066943 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1066894 AAAGGTCCGC
* *
1066904 AT AT AC AT AC 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
1066944 TTAAAAGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1067611 original size:3 final size:3
Alignment explanation
Indices: 1067599--1067648 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1067589 TAATAATATA
* * * *
1067599 ATG ATA ATG ATG ATG ATG ATA ATG ATG ATG AAG ATA ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1067647 AT
1 AT
1067649 AATAGTAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1067617 original size:15 final size:15
Alignment explanation
Indices: 1067599--1067651 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
1067589 TAATAATATA
1067599 ATGATAATGATGATG
1 ATGATAATGATGATG
1067614 ATGATAATGATGATG
1 ATGATAATGATGATG
*
1067629 AAGATAATGATGATG
1 ATGATAATGATGATG
1067644 ATGATAAT
1 ATGATAAT
1067652 AGTAATAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (15 bp):
ATGATAATGATGATG
Found at i:1071122 original size:6 final size:6
Alignment explanation
Indices: 1071102--1071146 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1071092 GTAATGCCAC
* * * *
1071102 TATACA TACATA TATATA TATATA TATACA TATACA TATACA TAT
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TAT
1071147 TTAATTAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (6 bp):
TATACA
Found at i:1071126 original size:12 final size:12
Alignment explanation
Indices: 1071102--1071146 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1071092 GTAATGCCAC
*
1071102 TATACATACATA
1 TATACATATATA
*
1071114 TATATATATATA
1 TATACATATATA
*
1071126 TATACATATACA
1 TATACATATATA
1071138 TATACATAT
1 TATACATAT
1071147 TTAATTAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (12 bp):
TATACATATATA
Found at i:1077745 original size:16 final size:16
Alignment explanation
Indices: 1077717--1077752 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1077707 GAATAATACT
1077717 ATTTTATTATTTTTAA
1 ATTTTATTATTTTTAA
1077733 ATTTT-TTATTTTTTAA
1 ATTTTATTA-TTTTTAA
1077749 ATTT
1 ATTT
1077753 GATAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTATTATTTTTAA
Found at i:1078012 original size:2 final size:2
Alignment explanation
Indices: 1078005--1078045 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1077995 GTATTCTCAT
* *
1078005 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1078046 TGAATTACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1078562 original size:11 final size:11
Alignment explanation
Indices: 1078546--1078584 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1078536 AATAAAAAAA
1078546 TATATTATATT
1 TATATTATATT
1078557 TATATTAT-TT
1 TATATTATATT
* *
1078567 TTTATTATAAT
1 TATATTATATT
1078578 TATATTA
1 TATATTA
1078585 AAAATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATATT
Found at i:1078736 original size:15 final size:16
Alignment explanation
Indices: 1078716--1078745 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1078706 TATATGTATA
1078716 TATTTTTTA-TAATAG
1 TATTTTTTATTAATAG
1078731 TATTTTTTATTAATA
1 TATTTTTTATTAATA
1078746 TTTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TATTTTTTATTAATAG
Found at i:1078835 original size:23 final size:23
Alignment explanation
Indices: 1078807--1078856 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1078797 GTAAATTTTG
1078807 ATTTATTTGTTTAT-TCACGTCAT
1 ATTTATTT-TTTATGTCACGTCAT
* *
1078830 ATTTATTTTTTATGTTATGTCAT
1 ATTTATTTTTTATGTCACGTCAT
1078853 ATTT
1 ATTT
1078857 TAATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTATTTTTTATGTCACGTCAT
Found at i:1079688 original size:26 final size:26
Alignment explanation
Indices: 1079652--1079704 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1079642 TTTTTTATAT
* *
1079652 TATATTTATATTTAAAATATT-ACATA
1 TATATATATATATAAAAT-TTAACATA
1079678 TATATATATATATAAAATTTAACATA
1 TATATATATATATAAAATTTAACATA
1079704 T
1 T
1079705 TAATAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATATATATATAAAATTTAACATA
Found at i:1080142 original size:22 final size:23
Alignment explanation
Indices: 1080098--1080143 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1080088 AAAAGTATTG
*
1080098 AATAAAAAATATTATAATGATTA
1 AATAAAAAATATTATAATAATTA
**
1080121 AATAAAAAA-ATTATGTTAATTA
1 AATAAAAAATATTATAATAATTA
1080143 A
1 A
1080144 TATTATATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAAAAAATATTATAATAATTA
Found at i:1080404 original size:18 final size:18
Alignment explanation
Indices: 1080381--1080446 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 18
1080371 GTATTTTACA
1080381 TAATTTATTATATTAATT
1 TAATTTATTATATTAATT
1080399 TAATTTTAATTATA--AATT
1 TAA-TTT-ATTATATTAATT
* *
1080417 TAAATTATTTTATT--TT
1 TAATTTATTATATTAATT
1080433 ATAATTTATT-TATT
1 -TAATTTATTATATT
1080447 TTATTACACA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
16 11 0.28
17 10 0.25
18 10 0.25
19 3 0.08
20 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTTATTATATTAATT
Found at i:1080419 original size:23 final size:23
Alignment explanation
Indices: 1080393--1080449 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
1080383 ATTTATTATA
1080393 TTAATTTAATTTTAATTATA-AAT
1 TTAATTT-ATTTTAATTATATAAT
* *
1080416 TTAAATTATTTT-ATTTTATAAT
1 TTAATTTATTTTAATTATATAAT
1080438 TT-ATTTATTTTA
1 TTAATTTATTTTA
1080450 TTACACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 13 0.45
22 10 0.34
23 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAATTTATTTTAATTATATAAT
Found at i:1082313 original size:34 final size:34
Alignment explanation
Indices: 1082275--1082350 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
1082265 ATCCATTTAG
*
1082275 TCAACAATGGCAAACTACCAAATCACCCATTCAA
1 TCAACAATGGCAAACCACCAAATCACCCATTCAA
* * *
1082309 TCAACAATGGCAAACCATCAAATCACCCATTTAG
1 TCAACAATGGCAAACCACCAAATCACCCATTCAA
1082343 TCAACAAT
1 TCAACAAT
1082351 TCTCTCACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (34 bp):
TCAACAATGGCAAACCACCAAATCACCCATTCAA
Found at i:1087739 original size:20 final size:20
Alignment explanation
Indices: 1087703--1087750 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
1087693 ATAATATTAT
1087703 TTATATATTATATAAATATA
1 TTATATATTATATAAATATA
1087723 TTATA-ATTATATAAAATATA
1 TTATATATTATAT-AAATATA
1087743 TTATATAT
1 TTATATAT
1087751 GCATACGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.27
20 17 0.65
21 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATATTATATAAATATA
Found at i:1090043 original size:23 final size:19
Alignment explanation
Indices: 1090009--1090055 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
1089999 TAATTATATA
1090009 ATATATATTAATTTTATATTT
1 ATATATATTAATTTT-TA-TT
1090030 ATATATTATGTAATTTTTATT
1 ATATA-TAT-TAATTTTTATT
1090051 ATATA
1 ATATA
1090056 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATATATTAATTTTTATT
Found at i:1090097 original size:21 final size:21
Alignment explanation
Indices: 1090060--1090099 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1090050 TATATAAAAA
*
1090060 ATAAATATATAATAATATAAT
1 ATAAATATATAAAAATATAAT
1090081 ATAAATA-ATAAAAAATATA
1 ATAAATATAT-AAAAATATA
1090100 TTAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATATATAAAAATATAAT
Found at i:1090203 original size:21 final size:22
Alignment explanation
Indices: 1090125--1090208 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 22
1090115 TTTAAAATTA
*
1090125 ATAAAAAAATTATTAAAT-TAAT
1 ATAAAAAAATT-TAAAATATAAT
* *
1090147 AAAAAATCAAATTTTTAAAATATATT
1 ATAAAA--AAA--TTTAAAATATAAT
*
1090173 TTAAAAAAATTTAAAA-ATAAT
1 ATAAAAAAATTTAAAATATAAT
*
1090194 ATAAATAAATTTAAA
1 ATAAAAAAATTTAAA
1090209 TTATTTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
21 17 0.35
22 12 0.24
24 6 0.12
25 5 0.10
26 9 0.18
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAAAATTTAAAATATAAT
Found at i:1090255 original size:31 final size:32
Alignment explanation
Indices: 1090191--1090264 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
1090181 ATTTAAAAAT
* *
1090191 AATATAAAT-AAATTTAAATTATTTTTTTATA
1 AATATAAATAAAATTTAAATAATTTATTTATA
1090222 AATATAAATAAAATTTAAA-AATTATATTT-TA
1 AATATAAATAAAATTTAAATAATT-TATTTATA
1090253 AAT-TAAACTAAA
1 AATATAAA-TAAA
1090265 TATAAACAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.11
31 21 0.55
32 13 0.34
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATAAATAAAATTTAAATAATTTATTTATA
Found at i:1093637 original size:35 final size:35
Alignment explanation
Indices: 1093578--1093646 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
1093568 TATCCACTTA
*
1093578 TATATAAATTATTTTTTTAATATGATTATATTAAAAT
1 TATATAAATTATTTTTTT-ATATGA-TATAATAAAAT
1093615 TATATAAA-TATTTTTATT-TATGATATAATAAA
1 TATATAAATTATTTTT-TTATATGATATAATAAA
1093647 TAAAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 8 0.27
35 5 0.17
36 7 0.23
37 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TATATAAATTATTTTTTTATATGATATAATAAAAT
Found at i:1095774 original size:2 final size:2
Alignment explanation
Indices: 1095761--1095813 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1095751 AAAAAGTAAA
*
1095761 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1095803 AG AG AG AG AG A
1 AG AG AG AG AG A
1095814 TCCCCAGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1096348 original size:2 final size:2
Alignment explanation
Indices: 1096343--1096384 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1096333 ATATATATAT
1096343 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1096385 GTGGTGTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1101182 original size:12 final size:13
Alignment explanation
Indices: 1101153--1101185 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1101143 ATTATTTACA
1101153 TATT-TTAAAATT
1 TATTATTAAAATT
1101165 TATTATTAAAATT
1 TATTATTAAAATT
1101178 T-TTATTAA
1 TATTATTAA
1101186 TTAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTAAAATT
Found at i:1109476 original size:20 final size:20
Alignment explanation
Indices: 1109451--1109506 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1109441 CTGCCAAGAA
1109451 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
1109471 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
1109491 AATGTATCGATACATT
1 AATGTATCGATACATT
1109507 GTATCGATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:1109511 original size:13 final size:13
Alignment explanation
Indices: 1109493--1109520 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1109483 CATTATTCAA
1109493 TGTATCGATACAT
1 TGTATCGATACAT
1109506 TGTATCGATACAT
1 TGTATCGATACAT
1109519 TG
1 TG
1109521 ATCTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1113903 original size:20 final size:20
Alignment explanation
Indices: 1113878--1113934 Score: 98
Period size: 19 Copynumber: 2.9 Consensus size: 20
1113868 TACTGCCAGT
1113878 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAATTG
1113898 TTCATGTATCGATACAA-TG
1 TTCATGTATCGATACAATTG
*
1113917 ATCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
1113935 GTATCAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:1113965 original size:33 final size:32
Alignment explanation
Indices: 1113901--1113965 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1113891 ACAATTGTTC
* * * *
1113901 ATGTATCGATACAATGATCATGTATCGATACA
1 ATGTATCAATACAAAGATAATATATCGATACA
1113933 ATGTATCAATACAAAGCATAATATATCGATACA
1 ATGTATCAATACAAAG-ATAATATATCGATACA
1113966 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (32 bp):
ATGTATCAATACAAAGATAATATATCGATACA
Found at i:1119248 original size:122 final size:122
Alignment explanation
Indices: 1119031--1119276 Score: 456
Period size: 122 Copynumber: 2.0 Consensus size: 122
1119021 GAGATTTGAC
* *
1119031 ATGAATCCTGATCACTTATGATGCAAAAAACTCGTTTCGCAAAGGAAGAAAATGTCCTGAAATAT
1 ATGAATCCCGATCACTTATGATGCAAAAAACTCGTTTCGCAAAGGAAGAAAATGTCCCGAAATAT
1119096 GAAAATTTACCTGCATGTATCGATACATTGAATGATGTATCGATACATCTGGGTAAA
66 GAAAATTTACCTGCATGTATCGATACATTGAATGATGTATCGATACATCTGGGTAAA
*
1119153 ATGAATCCCGATCACTTATGATGCAAAAAACTCGTTTGGCAAAGGAAGAAAATGTCCCGAAATAT
1 ATGAATCCCGATCACTTATGATGCAAAAAACTCGTTTCGCAAAGGAAGAAAATGTCCCGAAATAT
*
1119218 GAAAATTTGCCTGCATGTATCGATACATTGAATGATGTATCGATACATCTGGGTAAA
66 GAAAATTTACCTGCATGTATCGATACATTGAATGATGTATCGATACATCTGGGTAAA
1119275 AT
1 AT
1119277 TCCCAGATGT
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (122 bp):
ATGAATCCCGATCACTTATGATGCAAAAAACTCGTTTCGCAAAGGAAGAAAATGTCCCGAAATAT
GAAAATTTACCTGCATGTATCGATACATTGAATGATGTATCGATACATCTGGGTAAA
Found at i:1119336 original size:20 final size:20
Alignment explanation
Indices: 1119283--1119337 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1119273 AAATTCCCAG
**
1119283 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
1119303 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
1119323 ATGTATCGATACATT
1 ATGTATCGATACATT
1119338 TCCTTGACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:1120146 original size:13 final size:13
Alignment explanation
Indices: 1120128--1120153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1120118 ATAGTAACCC
1120128 ATGTATCGATACA
1 ATGTATCGATACA
1120141 ATGTATCGATACA
1 ATGTATCGATACA
1120154 TTCTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1120572 original size:18 final size:18
Alignment explanation
Indices: 1120549--1120584 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1120539 TTTGTCAAGT
*
1120549 GGTTTAGTTAAAATGTCA
1 GGTTTAGTGAAAATGTCA
1120567 GGTTTAGTGAAAATGTCA
1 GGTTTAGTGAAAATGTCA
1120585 ACTAGTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (18 bp):
GGTTTAGTGAAAATGTCA
Done.