Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009136.1 Hibiscus syriacus cultivar Beakdansim tig00112636_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: 240531
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1254 original size:79 final size:78
Alignment explanation
Indices: 1093--1266 Score: 181
Period size: 79 Copynumber: 2.2 Consensus size: 78
1083 AAAGATAACA
* * * * * *
1093 ATAAAAATAATAATGGTAAGCTAATATGTCTAAAAACAAGTGCAACTAAATCTCCAGGTCGATAA
1 ATAAAAACAATAATGATAAGCTAATATGTCTAAAAACAAGTGAAACAAAATATCCA-GTCAATAA
*
1158 TCAAACCAACTGCT
65 TCAAACCAACTACT
* * *
1172 ATAAAAACAATAATGATAAGTTAATATGTCTAAAAATCATGTGAAACAAAATATTCA-TACTAAT
1 ATAAAAACAATAATGATAAGCTAATATGTCTAAAAA-CAAGTGAAACAAAATATCCAGT-C-AAT
* *
1236 AATCAAATC-ACTATT
63 AATCAAACCAACTACT
*
1251 ATAAAAACAACAATGA
1 ATAAAAACAATAATGA
1267 AAACAATAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
78 1 0.01
79 53 0.67
80 25 0.32
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (78 bp):
ATAAAAACAATAATGATAAGCTAATATGTCTAAAAACAAGTGAAACAAAATATCCAGTCAATAAT
CAAACCAACTACT
Found at i:6632 original size:18 final size:18
Alignment explanation
Indices: 6570--6633 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
6560 TTTATTGAAA
*
6570 AACCGATAAACCGAACCG
1 AACCGAAAAACCGAACCG
*
6588 AACTGAAAAACCTGAACCG
1 AACCGAAAAACC-GAACCG
6607 TTAA---AAAAACCGAACCG
1 --AACCGAAAAACCGAACCG
6624 AACCGAAAAA
1 AACCGAAAAA
6634 TCAGTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.16
18 22 0.58
19 6 0.16
21 2 0.05
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.08
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:9712 original size:29 final size:29
Alignment explanation
Indices: 9670--9728 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
9660 ATTTTCACCT
9670 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
9699 AACTAAATTGATGTAAGTAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
9728 A
1 A
9729 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:14323 original size:29 final size:29
Alignment explanation
Indices: 14281--14339 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
14271 ATTTTCACCT
14281 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
14310 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
14339 A
1 A
14340 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:14651 original size:13 final size:13
Alignment explanation
Indices: 14631--14663 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
14621 GCTCTTTGGG
14631 TAATAAAAAATAA
1 TAATAAAAAATAA
*
14644 TTATAAAAAATAA
1 TAATAAAAAATAA
14657 TAATAAA
1 TAATAAA
14664 GTAATTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAAAAAATAA
Found at i:14869 original size:2 final size:2
Alignment explanation
Indices: 14862--14886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14852 TCTTTTAAAT
14862 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14887 TATGAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25160 original size:30 final size:30
Alignment explanation
Indices: 25126--25200 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
25116 TTATGGTATC
25126 AGTCCTTATACTATTCTAAATTTGAAATAT
1 AGTCCTTATACTATTCTAAATTTGAAATAT
*
25156 AGTCCTTATACTATTCTCAATTTGAAATAT
1 AGTCCTTATACTATTCTAAATTTGAAATAT
25186 AGTCCTTATACTATT
1 AGTCCTTATACTATT
25201 GTTAATGTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (30 bp):
AGTCCTTATACTATTCTAAATTTGAAATAT
Found at i:28144 original size:2 final size:2
Alignment explanation
Indices: 28137--28161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28127 TACACATGTA
28137 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28162 GTTAGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28847 original size:20 final size:20
Alignment explanation
Indices: 28824--28864 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28814 ATTTACGAAA
*
28824 ATGACCAACAATTTCGCAAC
1 ATGAACAACAATTTCGCAAC
**
28844 ATGAACTCCAATTTCGCAAC
1 ATGAACAACAATTTCGCAAC
28864 A
1 A
28865 CAGGTTCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (20 bp):
ATGAACAACAATTTCGCAAC
Found at i:28897 original size:20 final size:20
Alignment explanation
Indices: 28874--28943 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
28864 ACAGGTTCCA
*
28874 AAATCGCAACGCAAATAGGT
1 AAATCGCAACGCAAATATGT
28894 AAATCGCAACG-ATAATATGT
1 AAATCGCAACGCA-AATATGT
* *
28914 AAATCGCAACACGAATATGT
1 AAATCGCAACGCAAATATGT
28934 AAATCGCAAC
1 AAATCGCAAC
28944 ACAGAAGTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCAAATATGT
Found at i:29019 original size:20 final size:20
Alignment explanation
Indices: 28994--29061 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
28984 AACAGTACTA
*
28994 TCGCAACGCGAATTTCGTTT
1 TCGCAACGCGAATTTCATTT
***
29014 TCGCAACGCG-ATTCTCCAAAA
1 TCGCAACGCGAATT-T-CATTT
29035 TCGCAACGCGAATTTCATTT
1 TCGCAACGCGAATTTCATTT
29055 TCGCAAC
1 TCGCAAC
29062 ACTAATTACC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 20 0.53
21 12 0.32
22 3 0.08
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGAATTTCATTT
Found at i:29128 original size:22 final size:22
Alignment explanation
Indices: 29093--29134 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29083 TTAGCGTTGC
29093 GAAATTCGAGTTGCGAATTTAGA
1 GAAATTCGAGTTGCG-ATTTAGA
*
29116 GAAA-TCGCGTTGCGATTTA
1 GAAATTCGAGTTGCGATTTA
29135 CATATTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (22 bp):
GAAATTCGAGTTGCGATTTAGA
Found at i:29370 original size:20 final size:20
Alignment explanation
Indices: 29347--29408 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
29337 GTGTTGGGAT
*
29347 TTACCTATTCGCGTTGTGAA
1 TTACCTATTCGCGTTGCGAA
* ** *
29367 TTACATATTATCGTTGCGAT
1 TTACCTATTCGCGTTGCGAA
*
29387 TTAACTATTCGCGTTGCGAA
1 TTACCTATTCGCGTTGCGAA
29407 TT
1 TT
29409 TGGAAAATCG
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
TTACCTATTCGCGTTGCGAA
Found at i:31497 original size:2 final size:2
Alignment explanation
Indices: 31490--31516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31480 CCGGCTCATC
31490 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31517 ATTTTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55186 original size:3 final size:3
Alignment explanation
Indices: 55178--55254 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
55168 CTCCGTTAAC
* * * *
55178 CTT CTT CTT CTT -TCT CTT CAT CTT CCT CTT CCT CTT CTT CTT CTC
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
55223 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
55255 AAGGAGCTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.02
3 62 0.97
4 1 0.02
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:56120 original size:31 final size:31
Alignment explanation
Indices: 56082--56177 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
56072 CTTTTTAGGT
*
56082 TTATAAATCAATAACATTAGTGATTAATTTG
1 TTATAAATCAATAACATTAGTGACTAATTTG
** *
56113 TTATAAATCAATAATGTTAGTGACTAGTTTG
1 TTATAAATCAATAACATTAGTGACTAATTTG
* *
56144 TTATAAATCGATAACATTAGTGACCAATTTG
1 TTATAAATCAATAACATTAGTGACTAATTTG
56175 TTA
1 TTA
56178 CTTTTGAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (31 bp):
TTATAAATCAATAACATTAGTGACTAATTTG
Found at i:56831 original size:20 final size:22
Alignment explanation
Indices: 56791--56847 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
56781 ATTTTATCAT
56791 AATATTATAAAATTAATTATTA
1 AATATTATAAAATTAATTATTA
56813 AATA-TATAAAATT-ATTATTA
1 AATATTATAAAATTAATTATTA
*
56833 AATGATTATTAAATT
1 AAT-ATTATAAAATT
56848 TATCAAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.31
21 10 0.31
22 12 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AATATTATAAAATTAATTATTA
Found at i:56840 original size:11 final size:10
Alignment explanation
Indices: 56776--56850 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 10
56766 TAAAATAATC
*
56776 ATTAAATTTT
1 ATTAAATATT
*
56786 ATCATAATATT
1 ATTA-AATATT
*
56797 ATAAAATTAATT
1 ATTAAA-T-ATT
56809 ATTAAATA-T
1 ATTAAATATT
*
56818 ATAAAATTATT
1 ATTAAA-TATT
56829 ATTAAATGATT
1 ATTAAAT-ATT
56840 ATTAAAT-TT
1 ATTAAATATT
56849 AT
1 AT
56851 CAAAATGTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 10 0.19
10 9 0.17
11 26 0.49
12 8 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (10 bp):
ATTAAATATT
Found at i:59948 original size:18 final size:18
Alignment explanation
Indices: 59884--59948 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
59874 TTTACCATTT
*
59884 TTATTTTTATTATTATTA
1 TTATTTTTATTATTACTA
* * *
59902 TTCTTTATATTA-TCCTTA
1 TTATTTTTATTATTAC-TA
*
59920 TTATTTCTATTATTACTA
1 TTATTTTTATTATTACTA
*
59938 TTTTTTTTATT
1 TTATTTTTATT
59949 TATTCATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 1 0.03
18 33 0.92
19 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTTATTATTACTA
Found at i:60187 original size:2 final size:2
Alignment explanation
Indices: 60182--60214 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
60172 TTTATGTATG
*
60182 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60215 TCATTTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60310 original size:17 final size:18
Alignment explanation
Indices: 60288--60326 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
60278 TCATTAATTA
*
60288 TTTATTCCATTTTTA-TT
1 TTTATTCCACTTTTACTT
*
60305 TTTATTCCCCTTTTACTT
1 TTTATTCCACTTTTACTT
60323 TTTA
1 TTTA
60327 CTATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTCCACTTTTACTT
Found at i:60435 original size:10 final size:9
Alignment explanation
Indices: 60409--60482 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 9
60399 TTTTACTTTT
60409 TATTTTATA
1 TATTTTATA
*
60418 TATTTTATG
1 TATTTTATA
60427 TATTTT-TA
1 TATTTTATA
* *
60435 TATTCTACA
1 TATTTTATA
*
60444 TA-TATATA
1 TATTTTATA
*
60452 TA-TATATA
1 TATTTTATA
*
60460 TATATATATA
1 TAT-TTTATA
*
60470 TATTTTATT
1 TATTTTATA
60479 TATT
1 TATT
60483 ATTTTCATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
8 20 0.37
9 25 0.46
10 9 0.17
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TATTTTATA
Found at i:60450 original size:2 final size:2
Alignment explanation
Indices: 60443--60472 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60433 TATATTCTAC
60443 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
60473 TTTATTTATT
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:68408 original size:20 final size:20
Alignment explanation
Indices: 68380--68417 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
68370 ATAGTATGAC
68380 TAATAAAATTAAAAAAATAG
1 TAATAAAATTAAAAAAATAG
*
68400 TAATCAAATTAAAAAAAT
1 TAATAAAATTAAAAAAAT
68418 TCATTGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TAATAAAATTAAAAAAATAG
Found at i:69243 original size:2 final size:2
Alignment explanation
Indices: 69236--69269 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
69226 CTGAAATTGA
69236 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
69270 TTCGAATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70760 original size:45 final size:45
Alignment explanation
Indices: 70635--70767 Score: 216
Period size: 47 Copynumber: 3.0 Consensus size: 45
70625 AGGTGTTTCT
* *
70635 GGGT-TTTCTATATATTATGTTCTAAC-TATCAAAGTTCAGTTCA
1 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTTCA
70678 GGGTGTTTCTTTATATTATATGTTCTAACACATCAAAGTTCAGTTCA
1 GGGTGTTTCTTTATA-T-TATGTTCTAACACATCAAAGTTCAGTTCA
70725 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTT
1 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTT
70768 ACTTGTCTTA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
43 4 0.05
44 9 0.11
45 28 0.33
46 12 0.14
47 31 0.37
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (45 bp):
GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTTCA
Found at i:80964 original size:6 final size:6
Alignment explanation
Indices: 80953--81496 Score: 917
Period size: 6 Copynumber: 92.2 Consensus size: 6
80943 ATCTATCACC
80953 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81001 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81049 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81097 TATGTA TATGTA TATGTA TATGTA TATGTA TATG-- TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81143 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81191 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81239 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81287 TATGTA T-TGTA TATGTA TATGTA TATGTA TATG-- TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
81332 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
* *
81380 TATGCA TATGTA TATGCA TATGTA TATGTA TATGTA TATGTA TA--TA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
* * * * * * *
81426 TATGCA TTTATA TATGTG TGTGT- T-TGTT TATGTT TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
* * *
81472 TGTGTT TATGTT TATGTA TATGTA T
1 TATGTA TATGTA TATGTA TATGTA T
81497 GTGTTTATGC
Statistics
Matches: 512, Mismatches: 17, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
4 15 0.03
5 7 0.01
6 490 0.96
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:81512 original size:18 final size:18
Alignment explanation
Indices: 81480--81515 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
81470 TATGTGTTTA
* *
81480 TGTTTATGTATATGTATG
1 TGTTTATGCAAATGTATG
81498 TGTTTATGCAAATGTATG
1 TGTTTATGCAAATGTATG
81516 CATTTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (18 bp):
TGTTTATGCAAATGTATG
Found at i:83382 original size:37 final size:37
Alignment explanation
Indices: 83318--83426 Score: 204
Period size: 37 Copynumber: 3.0 Consensus size: 37
83308 AAGGCCCCCT
83318 TGAATTGATAAAGATGTGTGTGT--ACACATGATACA
1 TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
83353 TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
1 TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
83390 TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
1 TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
83427 ATATGTGTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.32
37 49 0.68
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (37 bp):
TGAATTGATAAAGATGTGTGTGTGCACACATGATACA
Found at i:83443 original size:2 final size:2
Alignment explanation
Indices: 83436--83460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83426 AATATGTGTT
83436 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
83461 GTAGAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85602 original size:31 final size:30
Alignment explanation
Indices: 85552--85642 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 30
85542 TTCGTCAATA
85552 AAATTTA--AAAAAATT-TAAAATACTTATT
1 AAATTTATTAAAAAATTATAAAATA-TTATT
* *
85580 AAATTTATTAAAAGATTATAAAATTATTAAT
1 AAATTTATTAAAAAATTATAAAA-TATTATT
* *
85611 AAATTTATCT-AAATACTATAAAATAATTATT
1 AAATTTAT-TAAAAAATTATAAAAT-ATTATT
85642 A
1 A
85643 TAGTATCGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
28 7 0.13
30 8 0.15
31 34 0.65
32 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATTTATTAAAAAATTATAAAATATTATT
Found at i:86180 original size:41 final size:41
Alignment explanation
Indices: 86133--86457 Score: 470
Period size: 41 Copynumber: 7.7 Consensus size: 41
86123 TAGTTGAAAA
* *
86133 TCGCGTTGCAATAGTCTACAGTGTCATTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
86174 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
86215 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* * *
86256 TCGCGTTGCGACAGTGTACAGTGTCGTTGCGTAGTTTCGTTGCGACATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCG-A--TT--TT-C--CATT
* *
86305 TCGTGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
86346 TCGCGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
86387 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
86428 TCGCGTTGCGACAGTGTACAGTGTCGTTGC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGC
86458 ACAGTGTCGT
Statistics
Matches: 261, Mismatches: 15, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
41 216 0.83
42 1 0.00
43 1 0.00
44 4 0.02
46 4 0.02
47 1 0.00
48 1 0.00
49 33 0.13
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:86184 original size:20 final size:20
Alignment explanation
Indices: 86159--86266 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 20
86149 TACAGTGTCA
*
86159 TTGCGATTTTCCATTTCGCG
1 TTGCGATTTTCCATGTCGCG
* *
86179 TTGCGATAGTCTACA-GT-GTCG
1 TTGCGAT--TTTCCATGTCG-CG
*
86200 TTGCGATTTTCCATTTCGCG
1 TTGCGATTTTCCATGTCGCG
* *
86220 TTGCGATAGTCTACA-GT-GTCG
1 TTGCGAT--TTTCCATGTCG-CG
*
86241 TTGCGATTTTCCATCTCGCG
1 TTGCGATTTTCCATGTCGCG
86261 TTGCGA
1 TTGCGA
86267 CAGTGTACAG
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
19 8 0.12
20 28 0.42
21 22 0.33
22 8 0.12
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCCATGTCGCG
Found at i:86203 original size:21 final size:21
Alignment explanation
Indices: 86177--86247 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
86167 TTCCATTTCG
86177 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
86198 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
86216 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
86239 CGTTGCGAT
1 CGTTGCGAT
86248 TTTCCATCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.23
21 18 0.46
22 4 0.10
23 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:86342 original size:131 final size:136
Alignment explanation
Indices: 86178--86543 Score: 459
Period size: 131 Copynumber: 2.7 Consensus size: 136
86168 TCCATTTCGC
*
86178 GTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTT
1 GTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTT
*
86243 GCGATTTTCCATCTCGCGTTGCGACAGTGTACAGTGTCGTTGCG-TAGT-T-T-CGTTGCGACA-
66 GCGATTTTCCATCTCGCGTTGCGACAGTCTACAGTGTCGTTGCGATAGTCTCTCCGTTGCGACAG
*
86303 TCT-CGT
131 TCTAC-A
*
86309 GTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCATT
1 GTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTT
* * **
86374 GCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGA
66 GCGATTTTCCATCTCGCGTTGCGACAGTCTACAGTGTCGTTGCGATAGT-C-TCTC-CGTTGCGA
*
86439 CAGTGTACA
128 CAGTCTACA
* *
86448 G-TGTCG-T--TGCACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGAT-TACAGTGTCG
1 GTTG-CGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAG-TCTACAGTGTCG
** * *
86508 TTGCGATTTTCCAAAT-TCGTTGCGATAGTCTACAGT
64 TTGCGATTTTCCATCTCGCGTTGCGACAGTCTACAGT
86544 AAATTAAAAA
Statistics
Matches: 209, Mismatches: 15, Indels: 18
0.86 0.06 0.07
Matches are distributed among these distances:
131 104 0.50
132 2 0.01
135 20 0.10
136 63 0.30
137 1 0.00
138 13 0.06
139 5 0.02
140 1 0.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.37
Consensus pattern (136 bp):
GTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTT
GCGATTTTCCATCTCGCGTTGCGACAGTCTACAGTGTCGTTGCGATAGTCTCTCCGTTGCGACAG
TCTACA
Found at i:86354 original size:20 final size:20
Alignment explanation
Indices: 86329--86438 Score: 66
Period size: 20 Copynumber: 5.4 Consensus size: 20
86319 TGTACAGTGT
*
86329 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATGTCG
* *
86349 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATGTCG
* *
86369 TCATTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATGTCG
* *
86390 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATGTCG
*
86410 TCGTTGCGATTTTCCATCTCG
1 -CGTTGCGATTTTCCATGTCG
86431 CGTTGCGA
1 CGTTGCGA
86439 CAGTGTACAG
Statistics
Matches: 66, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
19 8 0.12
20 29 0.44
21 21 0.32
22 8 0.12
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCCATGTCG
Found at i:86435 original size:172 final size:172
Alignment explanation
Indices: 86133--86543 Score: 657
Period size: 172 Copynumber: 2.4 Consensus size: 172
86123 TAGTTGAAAA
* *
86133 TCGCGTTGCAATAGTCTACAGTGTCATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 TCGCGTTGCGATAGT-TACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
*
86198 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTT
65 CATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTT
** *
86263 GCGACAGTGTACAGTGTCGTTGCGTAGTTTCGTTGCGA-CATC
130 GCGACAGTGTACAGTGTCGTTGCACAGTGTCGTTGCGATCATC
*
86305 TCGTGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 TCGCGTTGCGATAGT-TACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
86370 CATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTT
65 CATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTT
86435 GCGACAGTGTACAGTGTCGTTGCACAGTGTCGTTGCGATTTTCCATC
130 GCGACAGTGTACAGTGTCGTTGCACAGTGTCGTTGCGA---T-CATC
*
86482 TCGCGTTGCGATAGATTACAGTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGATAG-TTACAGTGTCGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGT
86544 AAATTAAAAA
Statistics
Matches: 222, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
172 160 0.72
176 19 0.09
177 39 0.18
178 4 0.02
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (172 bp):
TCGCGTTGCGATAGTTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTC
ATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTG
CGACAGTGTACAGTGTCGTTGCACAGTGTCGTTGCGATCATC
Found at i:86463 original size:13 final size:13
Alignment explanation
Indices: 86445--86470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86435 GCGACAGTGT
86445 ACAGTGTCGTTGC
1 ACAGTGTCGTTGC
86458 ACAGTGTCGTTGC
1 ACAGTGTCGTTGC
86471 GATTTTCCAT
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:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
ACAGTGTCGTTGC
Found at i:86486 original size:54 final size:54
Alignment explanation
Indices: 86404--86511 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
86394 GCGATAGTCT
86404 ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGACAG-TGTACAGTGTCGTTGC
1 ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGACAGAT-TACAGTGTCGTTGC
*
86458 ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGATTACAGTGTCGTTGC
1 ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGACAGATTACAGTGTCGTTGC
86512 GATTTTCCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (54 bp):
ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGACAGATTACAGTGTCGTTGC
Found at i:86542 original size:40 final size:41
Alignment explanation
Indices: 86458--86543 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
86448 GTGTCGTTGC
**
86458 ACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGATT
1 ACAGTGTCGTTGCGATTTTCCAAATCGCGTTGCGATAGATT
*
86499 ACAGTGTCGTTGCGATTTTCCAAAT-TCGTTGCGATAG-TCT
1 ACAGTGTCGTTGCGATTTTCCAAATCGCGTTGCGATAGAT-T
86539 ACAGT
1 ACAGT
86544 AAATTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 1 0.02
40 17 0.41
41 23 0.56
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ACAGTGTCGTTGCGATTTTCCAAATCGCGTTGCGATAGATT
Found at i:86621 original size:6 final size:6
Alignment explanation
Indices: 86610--86641 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
86600 TGACACGTAT
*
86610 GACCAC GACCAC GACCAC GCCCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GA
86642 GACGAGACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:87316 original size:21 final size:21
Alignment explanation
Indices: 87290--87360 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
87280 AATTTGGAAA
87290 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTACACT
* * *
87311 ATCGCAACG-CGAAATGGA-A-A
1 ATCGCAACGAC--ACTGTACACT
87331 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTACACT
*
87352 ACCGCAACG
1 ATCGCAACG
87361 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 4 0.11
20 11 0.29
21 19 0.50
22 4 0.11
ACGTcount: A:0.37, C:0.31, G:0.18, T:0.14
Consensus pattern (21 bp):
ATCGCAACGACACTGTACACT
Found at i:87337 original size:41 final size:41
Alignment explanation
Indices: 87284--87420 Score: 197
Period size: 41 Copynumber: 3.3 Consensus size: 41
87274 GCAACGAATT
87284 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
*
87325 TGGAAAATCGCAACGACACTGTACACTACCGCAACGCGAAA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
* * *
87366 TGGAATATCGCAACG-CGA-TTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGAC-ACTGTAC-ACTATCGCAACGCGAAA
*
87407 TGAAAAATCGCAAC
1 TGGAAAATCGCAAC
87421 TCAAAATGGA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 4 0.05
41 83 0.95
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (41 bp):
TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
Found at i:87419 original size:61 final size:61
Alignment explanation
Indices: 87354--87486 Score: 212
Period size: 61 Copynumber: 2.2 Consensus size: 61
87344 TGTACACTAC
*
87354 CGCAACGCGAAATGGAATATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAAT
1 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAAT
* * * * *
87415 CGCAACTCAAAATGGAAAATCGCAACGCGATTTTTAATTATCGCAACGCGAAATGGAAAAT
1 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAAT
87476 CGCAACGCGAA
1 CGCAACGCGAA
87487 TTTGCGATGC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (61 bp):
CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAAT
Found at i:87500 original size:13 final size:13
Alignment explanation
Indices: 87482--87507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87472 AAATCGCAAC
87482 GCGAATTTGCGAT
1 GCGAATTTGCGAT
87495 GCGAATTTGCGAT
1 GCGAATTTGCGAT
87508 ACTGGAGATC
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:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
GCGAATTTGCGAT
Found at i:87526 original size:20 final size:20
Alignment explanation
Indices: 87501--87546 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
87491 CGATGCGAAT
* *
87501 TTGCGATACTGGAGATCGCG
1 TTGCGATACTAGAGATCGCA
*
87521 TTGCGA-ATTAGAGATCGCA
1 TTGCGATACTAGAGATCGCA
87540 TTGCGAT
1 TTGCGAT
87547 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TTGCGATACTAGAGATCGCA
Found at i:91035 original size:2 final size:2
Alignment explanation
Indices: 91028--91052 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91018 AAATAAATAA
91028 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
91053 ATTGTAACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91231 original size:2 final size:2
Alignment explanation
Indices: 91224--91260 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
91214 CTTCAAATCC
*
91224 TA TA TA TA TA TA TA TA TA T- TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91261 GTTAACAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:96073 original size:130 final size:130
Alignment explanation
Indices: 95927--96174 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
95917 TATTTATATA
* ** *
95927 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* * * *
95992 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACTTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
96057 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* * *
96122 TTAACACATGATCATGATATATGTTATTAGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTA
96175 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:96205 original size:130 final size:129
Alignment explanation
Indices: 95941--96205 Score: 282
Period size: 130 Copynumber: 2.0 Consensus size: 129
95931 ATTTGGTCCT
* ** * *
95941 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* * * *** * * **** *
96006 TGACACGTGTCATTGGTGACACATGTCACCACTTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
96071 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* * * *
96136 TGATATATGTTATTAGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTAGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
96200 -A
128 CA
96201 AAATT
1 AAATT
96206 TGGGTCTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
130 97 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:96534 original size:28 final size:27
Alignment explanation
Indices: 96503--96565 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
96493 AGTTGATACA
*
96503 ATATTTTAAAAGAATAAATTTAATATTT
1 ATATTTTAAAA-AATAAATTTAATAATT
** *
96531 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAATAATT
96559 ATATTTT
1 ATATTTT
96566 TCATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAATAATT
Found at i:96666 original size:16 final size:18
Alignment explanation
Indices: 96645--96678 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
96635 ATTTCTTATT
96645 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
96661 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
96679 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:97205 original size:21 final size:21
Alignment explanation
Indices: 97175--97225 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
97165 CTCAAACTCC
* * *
97175 AAACCCTAAATCATATACTCT
1 AAACCTTAAATCATAAACCCT
* *
97196 AAATCTTAAATCTTAAACCCT
1 AAACCTTAAATCATAAACCCT
97217 AAACCTTAA
1 AAACCTTAA
97226 CTCTAAAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (21 bp):
AAACCTTAAATCATAAACCCT
Found at i:100599 original size:30 final size:29
Alignment explanation
Indices: 100559--100625 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 29
100549 TTCTGGAATT
* *
100559 TGAATGACTGTAATTTGAATTATTAGAAAA
1 TGAATTACTGTAATTTGAATT-CTAGAAAA
*
100589 TGAATTACTGTAATTTGAATTCTGGAAAA
1 TGAATTACTGTAATTTGAATTCTAGAAAA
100618 TGAATTAC
1 TGAATTAC
100626 ATTTTTGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.41
30 20 0.59
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (29 bp):
TGAATTACTGTAATTTGAATTCTAGAAAA
Found at i:100607 original size:15 final size:15
Alignment explanation
Indices: 100555--100609 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
100545 GGTTTTCTGG
*
100555 AATTTGAATGACTGT
1 AATTTGAATTACTGT
*
100570 AATTTGAATTATTAG-
1 AATTTGAATTACT-GT
**
100585 AAAATGAATTACTGT
1 AATTTGAATTACTGT
100600 AATTTGAATT
1 AATTTGAATT
100610 CTGGAAAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (15 bp):
AATTTGAATTACTGT
Found at i:100623 original size:14 final size:15
Alignment explanation
Indices: 100574--100625 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
100564 GACTGTAATT
* *
100574 TGAATTATTAGAAAA
1 TGAATTACTGGAAAA
* **
100589 TGAATTACTGTAATT
1 TGAATTACTGGAAAA
100604 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
100618 TGAATTAC
1 TGAATTAC
100626 ATTTTTGGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:100937 original size:19 final size:19
Alignment explanation
Indices: 100913--100983 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
100903 TCAAATATCT
*
100913 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
100932 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
100951 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
100971 TTATTAAATATAT
1 TTATTAAA-ATAT
100984 AAAAAAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:100964 original size:24 final size:26
Alignment explanation
Indices: 100937--101126 Score: 76
Period size: 28 Copynumber: 7.1 Consensus size: 26
100927 TTAGATTATT
100937 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
*
100961 ATATTATTCATTATTAAATATATAAAAAA
1 ATATTA-T-ATTATTAAATATAT-AAATA
*
100990 ATTATTATATATTTATTAAA-ATAAAAAT-
1 A-TA-T-TATA-TTATTAAATATATAAATA
* * *
101018 ATAATATCTTA-T-ATTATTATAATATA
1 ATATTATATTATTAAATA-TATAA-ATA
* *
101044 ATTGATTATTTTATTATAATATTAAAAATATA
1 A-T-ATTATATTATTA-AATA-T-ATAA-ATA
*
101076 ATATTATATTATTATAA-ATATTAATA
1 ATATTATATTATTA-AATATATAAATA
* *
101102 A-A-TATATT-TTAAATATTTTAATA
1 ATATTATATTATTAAATATATAAATA
101125 AT
1 AT
101127 TAATATTTCG
Statistics
Matches: 130, Mismatches: 15, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
22 3 0.02
23 14 0.11
24 19 0.15
25 6 0.05
26 5 0.04
27 6 0.05
28 21 0.16
29 10 0.08
30 20 0.15
31 16 0.12
32 10 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:101002 original size:27 final size:28
Alignment explanation
Indices: 100938--101002 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
100928 TAGATTATTA
*
100938 TATTA-ATATTAAATATATAAATAATAT
1 TATTATATATTAAATATATAAATAAAAT
100965 TATTCAT-TATTAAATATATAAA-AAAAT
1 TATT-ATATATTAAATATATAAATAAAAT
100992 TATTATATATT
1 TATTATATATT
101003 TATTAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 2 0.06
27 16 0.47
28 16 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTATATATTAAATATATAAATAAAAT
Found at i:101083 original size:22 final size:23
Alignment explanation
Indices: 101055--101101 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
101045 TTGATTATTT
101055 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
101077 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
101100 TA
1 TA
101102 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:101106 original size:22 final size:22
Alignment explanation
Indices: 101062--101118 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
101052 TTTTATTATA
* *
101062 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
101083 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
101105 ATATTTTAAATATT
1 ATATTATAAATATT
101119 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:105837 original size:2 final size:2
Alignment explanation
Indices: 105830--105880 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
105820 CATGCATAAG
105830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
105872 TA TA TA TA T
1 TA TA TA TA T
105881 GCCATTGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:108592 original size:18 final size:18
Alignment explanation
Indices: 108569--108607 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
108559 TTTTTTTTCC
*
108569 TTTATATGTACATACATA
1 TTTATATATACATACATA
*
108587 TTTATATATATATACATA
1 TTTATATATACATACATA
108605 TTT
1 TTT
108608 TGAAACTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATATATACATACATA
Found at i:108718 original size:39 final size:38
Alignment explanation
Indices: 108671--108815 Score: 122
Period size: 41 Copynumber: 3.8 Consensus size: 38
108661 TAGTTTAAAA
* *
108671 AAAACATTTTAGAAAATATATGTAGTATATA-A-TTTTTT
1 AAAACATTTT-GAAAATATATATA-TATATATAGTTTTTG
108709 AAAATCATTTTGAAAACTTATATATATATATATAGTTTTTG
1 AAAA-CATTTTGAAAA--TATATATATATATATAGTTTTTG
*
108750 AAAACATTTTTG-AAA-ACATATATAT-TATAG-TTTTG
1 AAAACA-TTTTGAAAATATATATATATATATAGTTTTTG
* * * * *
108785 AAAATATTTTAAAAACATTTATATATTTATA
1 AAAACATTTTGAAAATATATATATATATATA
108816 TATTATATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
34 4 0.04
35 13 0.14
36 13 0.14
37 13 0.14
38 9 0.10
39 12 0.13
40 13 0.14
41 14 0.15
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
AAAACATTTTGAAAATATATATATATATATAGTTTTTG
Found at i:108757 original size:79 final size:76
Alignment explanation
Indices: 108671--108818 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 76
108661 TAGTTTAAAA
* * * * *
108671 AAAACATTTTAGAAAATATATGTAGTATATAATTTTTTAAAATCATTTTGAAAAC-TTATATATA
1 AAAACATTTTAGAAAACATATATA-T-TAT-AGTTTTGAAAAT-ATTTTAAAAACATTATATATA
108735 TATATATAGTTTTTG
62 TATATATAGTTTTTG
* *
108750 AAAACATTTTTGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACATTTATATATTTAT
1 AAAACATTTTAGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACA-TTATATATATAT
108815 ATAT
65 ATAT
108819 TATATGTTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 10 0.17
76 10 0.17
77 18 0.30
78 1 0.02
79 21 0.35
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (76 bp):
AAAACATTTTAGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACATTATATATATATA
TATAGTTTTTG
Found at i:108759 original size:12 final size:12
Alignment explanation
Indices: 108744--108768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108734 ATATATATAG
108744 TTTTTGAAAACA
1 TTTTTGAAAACA
108756 TTTTTGAAAACA
1 TTTTTGAAAACA
108768 T
1 T
108769 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:108784 original size:35 final size:36
Alignment explanation
Indices: 108618--108810 Score: 128
Period size: 34 Copynumber: 5.2 Consensus size: 36
108608 TGAAACTACG
* * *
108618 TATATAATATATAGTTTTT-AATA-GTTTTTAAAAC-
1 TATAT-ATATATAGTTTTTGAAAACATTTTAAAAACA
*** *
108652 TATATA-ATATAGTTTAAAAAAAACATTTTAGAAAATA
1 TATATATATATAGTTT-TTGAAAACATTTTA-AAAACA
* * * *
108689 TATGTAGTATATAATTTTTTAAAATCATTTTGAAAACTTATA
1 TATATA-TATATAGTTTTTGAAAA-CATTTT-AAAA---ACA
*
108731 TATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATATATATAGTTTTTGAAAACA-TTTTAAAAACA
*
108768 TATATAT-TATAG-TTTTGAAAATATTTTAAAAACA
1 TATATATATATAGTTTTTGAAAACATTTTAAAAACA
*
108802 TTTATATAT
1 TATATATAT
108811 TTATATATTA
Statistics
Matches: 126, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
32 9 0.07
33 1 0.01
34 24 0.19
35 15 0.12
36 9 0.07
37 14 0.11
38 4 0.03
39 17 0.13
40 6 0.05
41 19 0.15
42 8 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATATATATAGTTTTTGAAAACATTTTAAAAACA
Found at i:108853 original size:53 final size:53
Alignment explanation
Indices: 108768--108921 Score: 160
Period size: 52 Copynumber: 3.0 Consensus size: 53
108758 TTTGAAAACA
* * * *
108768 TATATATTATA-G-TTTTGAAAATATTTTAAAAACATTTATATATTTATATA-T
1 TATAT-TTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATACT
* *
108819 TATATGTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTTTGAAAACT
1 TATAT-TTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTAT--ATACT
*
108875 TATA--TA-ATATTTTTGAAAACATGTTGAAAACATTTGTATA-TTATATA
1 TATATTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATA
108922 GTTTAAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
49 2 0.02
51 13 0.15
52 34 0.39
53 32 0.36
55 2 0.02
56 5 0.06
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (53 bp):
TATATTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATACT
Found at i:108871 original size:20 final size:22
Alignment explanation
Indices: 108846--108896 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
108836 TGAAAACATG
*
108846 TTGAAAACATT-TGT-ATATTT
1 TTGAAAACATTATATAATATTT
108866 TTGAAAAC-TTATATAATATTT
1 TTGAAAACATTATATAATATTT
108887 TTGAAAACAT
1 TTGAAAACAT
108897 GTTGAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 14 0.52
22 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
TTGAAAACATTATATAATATTT
Found at i:109046 original size:15 final size:15
Alignment explanation
Indices: 109007--109049 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
108997 TCTATTATTA
* *
109007 TTTATTTTAATTTAT
1 TTTAATTTATTTTAT
109022 TTTAATTTATTTTAT
1 TTTAATTTATTTTAT
109037 TTTAATTTATTTT
1 TTTAATTTATTTT
109050 TTTGGTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTAATTTATTTTAT
Found at i:109049 original size:10 final size:10
Alignment explanation
Indices: 109006--109045 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
108996 ATCTATTATT
109006 ATTTATTTTA
1 ATTTATTTTA
109016 ATTTATTTTA
1 ATTTATTTTA
109026 ATTTATTTTA
1 ATTTATTTTA
* *
109036 TTTTAATTTA
1 ATTTATTTTA
109046 TTTTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTATTTTA
Found at i:110531 original size:6 final size:6
Alignment explanation
Indices: 110520--110546 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
110510 GAATCGAATT
110520 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
110547 TTAATTTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:111136 original size:17 final size:17
Alignment explanation
Indices: 111114--111158 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
111104 TACATAATGT
111114 GAAATTTGAGCGTGAAA
1 GAAATTTGAGCGTGAAA
*
111131 GAAATTTGATCGTGAAA
1 GAAATTTGAGCGTGAAA
*
111148 GAATTTTGAGC
1 GAAATTTGAGC
111159 AAGTTTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (17 bp):
GAAATTTGAGCGTGAAA
Found at i:117637 original size:20 final size:21
Alignment explanation
Indices: 117612--117663 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
117602 TTTTCCCAAT
*
117612 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
117632 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
117653 TCGCAATGCGA
1 TCGCAATGCGA
117664 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:117677 original size:20 final size:20
Alignment explanation
Indices: 117652--117765 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
117642 AATTGGGAAA
*
117652 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
117672 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
117692 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
117713 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
117733 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
117753 TTCGCAACGCGAT
1 ATCGCAACGCGAT
117766 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:117696 original size:61 final size:61
Alignment explanation
Indices: 117649--117765 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
117639 GCGAATTGGG
* * * *
117649 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
117710 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
117766 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:118348 original size:19 final size:19
Alignment explanation
Indices: 118307--118353 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
118297 TCGCAACGAG
*
118307 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
* *
118326 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
118345 AAAATCGCA
1 AAAATCGCA
118354 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.26, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:118448 original size:20 final size:19
Alignment explanation
Indices: 118349--118460 Score: 117
Period size: 19 Copynumber: 6.1 Consensus size: 19
118339 GAAACCAAAA
*
118349 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
118368 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
118382 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
118401 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
118420 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
118439 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
118459 TC
1 TC
118461 AACCTAAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.12
16 3 0.04
17 3 0.04
19 44 0.58
20 17 0.22
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:118458 original size:39 final size:38
Alignment explanation
Indices: 118357--118460 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 38
118347 AATCGCATTG
* *
118357 CGATTTTCATTTCGCGTTGCGAT--TC---TCTCGTTA
1 CGATTCTCATTTCGCGTTGCGATAGTCATTTCGCGTTA
* *
118390 CGATTTTCATTTCGCGTTGCGATAGTCATTTCGCGTTG
1 CGATTCTCATTTCGCGTTGCGATAGTCATTTCGCGTTA
* **
118428 CGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 CGATTCTCATT-TCGCGTTGCGATAGTCATTTC
118461 AACCTAAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
33 23 0.39
35 2 0.03
38 16 0.27
39 18 0.31
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (38 bp):
CGATTCTCATTTCGCGTTGCGATAGTCATTTCGCGTTA
Found at i:120009 original size:63 final size:63
Alignment explanation
Indices: 119910--120040 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
119900 GTTACGTGAT
119910 GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
*
119973 GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGTGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
120036 GAGGT
1 GAGGT
120041 GTCTACTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (63 bp):
GAGGTCAATGTCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:120366 original size:95 final size:89
Alignment explanation
Indices: 120207--120393 Score: 286
Period size: 93 Copynumber: 2.0 Consensus size: 89
120197 TAGATTGCTT
120207 AGTAAATTTATTCGTTGCTGCCAATACTGCTAAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGTTGCTGCCAATACTGCTAAAACTGTTTATTAACACTGTGAAGTTAGTATTT
120272 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTGTCTTTTGGTTGA
* *
120298 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATTC-GTTGCTGCCAATACTGCTAAAAC--TGT-TT-ATTAACACTGTGAAGTTAG
120362 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
61 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
120391 AGT
1 AGT
120394 TTTGAAATAT
Statistics
Matches: 89, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
91 17 0.19
92 17 0.19
93 27 0.30
94 2 0.02
95 26 0.29
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (89 bp):
AGTAAATTTATTCGTTGCTGCCAATACTGCTAAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGA
Found at i:120712 original size:42 final size:42
Alignment explanation
Indices: 120610--120814 Score: 178
Period size: 42 Copynumber: 4.9 Consensus size: 42
120600 CCCGACTCGC
* * * * *
120610 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * *
120652 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGACCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * * *
120694 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGCGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
120736 CTATCATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
** * *
120778 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGA
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGA
120815 TCCCGATTCA
Statistics
Matches: 124, Mismatches: 38, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
42 120 0.97
43 4 0.03
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:120794 original size:84 final size:84
Alignment explanation
Indices: 120610--120785 Score: 307
Period size: 84 Copynumber: 2.1 Consensus size: 84
120600 CCCGACTCGC
* *
120610 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
120675 CCCACCGTTCAAGAGACCA
66 CCCACCGTTCAAGAGACCA
* *
120694 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGCGGCCCCTATCATTCCTCGAGAGTCCTCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
120759 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGACCA
120778 CTGTCATC
1 CTGTCATC
120786 GTTGAAGAGG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGACCA
Found at i:122189 original size:14 final size:14
Alignment explanation
Indices: 122170--122205 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
122160 ATTGTTTAAT
122170 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
122184 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
122198 TGATTTGT
1 TGATTTGT
122206 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:122342 original size:19 final size:19
Alignment explanation
Indices: 122315--122358 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
122305 AAGTACTATT
*
122315 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
122334 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
122353 GCAACG
1 GCAACG
122359 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:122438 original size:33 final size:31
Alignment explanation
Indices: 122386--122481 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 31
122376 AATTAAATTC
* *
122386 GCGTTGCGATTTTTCATTTCACATTGCGATTCCC
1 GCGTTGCGA-TTTTCATTTCGCATTGCGATT--A
*
122420 TCGTTGCGATTTTCATTTCGCATTGCGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTA
122453 GCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
122482 AGTAATTTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
31 2 0.04
33 43 0.77
34 8 0.14
35 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTA
Found at i:122447 original size:19 final size:19
Alignment explanation
Indices: 122423--122481 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
122413 GATTCCCTCG
122423 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
122442 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
122456 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
122475 TTGCGAT
1 TTGCGAT
122482 AGTAATTTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
14 11 0.38
19 18 0.62
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:122500 original size:20 final size:19
Alignment explanation
Indices: 122453--122503 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
122443 TGCGAAATTA
** *
122453 GCGTTGCGATTTTCATTTC
1 GCGTTGCGATAGTAATTTC
*
122472 GCATTGCGATAGTAATTTCC
1 GCGTTGCGATAGTAATTT-C
122492 GCGTTGCGATAG
1 GCGTTGCGATAG
122504 ACATTAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (19 bp):
GCGTTGCGATAGTAATTTC
Found at i:126063 original size:19 final size:20
Alignment explanation
Indices: 126002--126071 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
125992 ATTCATTTGA
*
126002 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
126022 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATGG
126042 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
126061 CTATCGCAACG
1 CTATCGCAACG
126072 ACAAAATCGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 16 0.34
20 31 0.66
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:126138 original size:19 final size:19
Alignment explanation
Indices: 126097--126161 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
126087 GAAATGAAAA
126097 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
126113 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
126130 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
126149 TCGTATTGCGATT
1 TCGCATTGCGATT
126162 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 26 0.60
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:126192 original size:20 final size:20
Alignment explanation
Indices: 126167--126205 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
126157 CGATTCTCTC
126167 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
126187 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
126206 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:128209 original size:20 final size:20
Alignment explanation
Indices: 128186--128230 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
128176 AACTTAAAAG
128186 CGCAACACGAAAATGACTAT
1 CGCAACACGAAAATGACTAT
* * *
128206 CGCAACGCGGAAATGGCTAT
1 CGCAACACGAAAATGACTAT
128226 CGCAA
1 CGCAA
128231 TGCGAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.13
Consensus pattern (20 bp):
CGCAACACGAAAATGACTAT
Found at i:128266 original size:33 final size:33
Alignment explanation
Indices: 128224--128313 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 33
128214 GGAAATGGCT
128224 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* *
128257 ATCGCAATGCAAAAT-GAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * *
128289 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATAAAAATCGCA
128314 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 28 0.56
33 22 0.44
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:128271 original size:13 final size:14
Alignment explanation
Indices: 128240--128297 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
128230 ATGCGAAATA
128240 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
128254 AAAATCGCAATGCAAA
1 AAAATCGCAA--CGAC
128270 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
128286 AAAATCGCAACG
1 AAAATCGCAACG
128298 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 6 0.17
18 9 0.25
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:128331 original size:19 final size:19
Alignment explanation
Indices: 128309--128390 Score: 86
Period size: 18 Copynumber: 4.6 Consensus size: 19
128299 GAAACACAAA
128309 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
128328 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* * *
128346 TCGTACTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
128362 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
128379 TCGCATTGCGAT
1 TCGCATTGCGAT
128391 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 4 0.08
17 4 0.08
18 18 0.35
19 17 0.33
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:128918 original size:18 final size:18
Alignment explanation
Indices: 128897--128936 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
128887 CAGATGATGA
*
128897 CTCTGGGTGAGGTGATAG
1 CTCTGGGCGAGGTGATAG
*
128915 CTCTGGGCGAGGTGATGG
1 CTCTGGGCGAGGTGATAG
128933 CTCT
1 CTCT
128937 CGAAGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.42, T:0.28
Consensus pattern (18 bp):
CTCTGGGCGAGGTGATAG
Found at i:130280 original size:20 final size:20
Alignment explanation
Indices: 130255--130297 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
130245 AATAGTTTCT
130255 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
130275 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
130295 GAA
1 GAA
130298 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:130303 original size:20 final size:20
Alignment explanation
Indices: 130265--130333 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
130255 GAAAATGAAA
* **
130265 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
130285 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
130305 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
130325 ATCGCAACG
1 ATCGCAACG
130334 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:130624 original size:22 final size:22
Alignment explanation
Indices: 130594--130637 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
130584 GATGGAGATA
*
130594 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
130616 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
130638 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:130893 original size:61 final size:61
Alignment explanation
Indices: 130811--130948 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
130801 CGCTTTGAAA
* * * *
130811 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
130872 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
130933 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
130949 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:130917 original size:20 final size:20
Alignment explanation
Indices: 130811--130945 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
130801 CGCTTTGAAA
*
130811 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
130832 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
130852 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
130872 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
130893 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
130913 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
130933 ATCGCATTGCGAT
1 ATCGCATTGCGAT
130946 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:131056 original size:21 final size:21
Alignment explanation
Indices: 131016--131056 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
131006 ACTGTAGACC
**
131016 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
131037 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
131057 GCGAATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:136419 original size:6 final size:6
Alignment explanation
Indices: 136410--136449 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
136400 GATCATGATG
* * *
136410 ATGGAC ATGGAC ATGGAC ATGGTC ATGGTC ATGGTC ATGG
1 ATGGAC ATGGAC ATGGAC ATGGAC ATGGAC ATGGAC ATGG
136450 GGACGATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (6 bp):
ATGGAC
Found at i:136425 original size:12 final size:12
Alignment explanation
Indices: 136410--136449 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
136400 GATCATGATG
*
136410 ATGGACATGGAC
1 ATGGACATGGTC
136422 ATGGACATGGTC
1 ATGGACATGGTC
*
136434 ATGGTCATGGTC
1 ATGGACATGGTC
136446 ATGG
1 ATGG
136450 GGACGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (12 bp):
ATGGACATGGTC
Found at i:136793 original size:18 final size:19
Alignment explanation
Indices: 136764--136818 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
136754 ATTAATGTTG
136764 ATGATAAATCAATTATCTA
1 ATGATAAATCAATTATCTA
136783 ATGAT-AATCAATTATCTA
1 ATGATAAATCAATTATCTA
136801 ATGATAAATCAATTATCT
1 ATGATAAATCAATTATCT
136819 GTTCACTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.38
Consensus pattern (19 bp):
ATGATAAATCAATTATCTA
Found at i:143262 original size:32 final size:31
Alignment explanation
Indices: 143226--143302 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
143216 CGGGGCCGTG
*
143226 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
143258 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
143289 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
143303 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:143285 original size:63 final size:63
Alignment explanation
Indices: 143179--143302 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
143169 CCCTAAGGGA
* * ** *
143179 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
143242 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
143303 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:144202 original size:5 final size:5
Alignment explanation
Indices: 144192--144232 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
144182 AACGGTCAAC
*
144192 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
144233 AACGGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:144213 original size:22 final size:22
Alignment explanation
Indices: 144185--144239 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
144175 AACGGTCAAC
144185 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
144207 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
144229 GGTCAACGGTC
1 GGTCAACGGTC
144240 AAACCGATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:144283 original size:10 final size:10
Alignment explanation
Indices: 144238--144327 Score: 71
Period size: 10 Copynumber: 9.1 Consensus size: 10
144228 GGGTCAACGG
*
144238 TCAAACCGAT
1 TCAAACCGGT
*
144248 TCAGACCGG-
1 TCAAACCGGT
*
144257 TCAAATCGGT
1 TCAAACCGGT
*
144267 TCGAACCGGT
1 TCAAACCGGT
*
144277 TGAAACCGG-
1 TCAAACCGGT
144286 TCAAAACCGG-
1 TC-AAACCGGT
144296 TCAGAACCGGT
1 TCA-AACCGGT
*
144307 TGAAAACCGG-
1 T-CAAACCGGT
144317 TCAAACCGGT
1 TCAAACCGGT
144327 T
1 T
144328 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 16 0.25
10 39 0.62
11 7 0.11
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:144305 original size:30 final size:30
Alignment explanation
Indices: 144235--144326 Score: 102
Period size: 29 Copynumber: 3.1 Consensus size: 30
144225 GTCGGGTCAA
* * * *
144235 CGGTCA-AACCGATTCAGACCGGTCAAAT-
1 CGGTCAGAACCGGTTGAAACCGGTCAAAAC
144263 CGGTTC-GAACCGGTTGAAACCGGTCAAAAC
1 CGG-TCAGAACCGGTTGAAACCGGTCAAAAC
144293 CGGTCAGAACCGGTTGAAAACCGGTC-AAAC
1 CGGTCAGAACCGGTTG-AAACCGGTCAAAAC
144323 CGGT
1 CGGT
144327 TTCCAGCAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.05
29 22 0.40
30 21 0.38
31 9 0.16
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (30 bp):
CGGTCAGAACCGGTTGAAACCGGTCAAAAC
Found at i:146198 original size:15 final size:15
Alignment explanation
Indices: 146178--146209 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
146168 ACAAACCTGA
146178 TGGATGTTGATGTTC
1 TGGATGTTGATGTTC
146193 TGGATGTTGATGTTC
1 TGGATGTTGATGTTC
146208 TG
1 TG
146210 CCTTAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.47
Consensus pattern (15 bp):
TGGATGTTGATGTTC
Found at i:150609 original size:32 final size:32
Alignment explanation
Indices: 150573--150649 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
150563 CGGGGCCGTG
*
150573 GGGCCTACCTAAGAACAT-ATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
**
150605 GGGCCTACCCGAG-AATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
*
150636 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
150650 GTCACATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:150632 original size:63 final size:63
Alignment explanation
Indices: 150528--150649 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
150518 CTAAGGGAAC
* * ** *
150528 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAACAT
1 ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAT
* *
150591 ATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
150650 GTCACATTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (63 bp):
ATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAT
Found at i:151538 original size:7 final size:7
Alignment explanation
Indices: 151526--151552 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
151516 GTCAAAGAAA
151526 GTCAACG
1 GTCAACG
151533 GTCAACG
1 GTCAACG
151540 GTCAACG
1 GTCAACG
151547 GTCAAC
1 GTCAAC
151553 AGTCGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:151564 original size:5 final size:5
Alignment explanation
Indices: 151554--151615 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
151544 ACGGTCAACA
* * *
151554 GTCGG GTCGG GTCGG GTCAACG GTCGA GTCGG GTCGG GTCAACG GTCGG
1 GTCGG GTCGG GTCGG GTC--GG GTCGG GTCGG GTCGG GTC--GG GTCGG
151603 GTCGG GTCGG GTC
1 GTCGG GTCGG GTC
151616 AACGGTCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 39 0.83
7 8 0.17
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GTCGG
Found at i:151573 original size:22 final size:22
Alignment explanation
Indices: 151546--151622 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
151536 AACGGTCAAC
*
151546 GGTCAACAGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
151568 GGTCAACGGTCGAGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
151590 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
151612 GGTCAACGGTC
1 GGTCAACGGTC
151623 AAACCGATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:151657 original size:19 final size:18
Alignment explanation
Indices: 151614--151678 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
151604 TCGGGTCGGG
*
151614 TCAA-CGGTCAAACCGAT
1 TCAACCGGTCAAACCGGT
151631 TCAGACCGGTCAAACCGGT
1 TCA-ACCGGTCAAACCGGT
*
151650 TCGAACCGGTTGAAACCGG-
1 TC-AACCGG-TCAAACCGGT
151669 TCAAACCGGT
1 TC-AACCGGT
151679 TTCCAGCAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 27 0.66
20 9 0.22
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (18 bp):
TCAACCGGTCAAACCGGT
Found at i:151679 original size:19 final size:20
Alignment explanation
Indices: 151623--151679 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
151613 GTCAACGGTC
* * *
151623 AAACCGATTCAGACCGG-TC
1 AAACCGGTTCAAACCGGTTG
*
151642 AAACCGGTTCGAACCGGTTG
1 AAACCGGTTCAAACCGGTTG
151662 AAACCGG-TCAAACCGGTT
1 AAACCGGTTCAAACCGGTT
151680 TCCAGCAGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCAAACCGGTTG
Found at i:160120 original size:5 final size:5
Alignment explanation
Indices: 160110--160142 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
160100 ATCGGTCACA
160110 AAATT AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAA
160143 ATTTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Done.