Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003613.1 Hibiscus syriacus cultivar Beakdansim tig00007642_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: 110989
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2574 original size:2 final size:2
Alignment explanation
Indices: 2567--2591 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2557 TGTGAAGAAC
2567 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2592 TTCAAGCTTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2991 original size:16 final size:17
Alignment explanation
Indices: 2950--2991 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2940 ACTCAGTTTA
2950 TATCTATACATATAATAT
1 TATCTA-ACATATAATAT
* *
2968 TATTTAACCTATAA-AT
1 TATCTAACATATAATAT
2984 TATCTAAC
1 TATCTAAC
2992 TTAGAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 7 0.33
18 5 0.24
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
TATCTAACATATAATAT
Found at i:8788 original size:35 final size:36
Alignment explanation
Indices: 8716--8864 Score: 182
Period size: 35 Copynumber: 4.2 Consensus size: 36
8706 TGAAAGTATT
* **
8716 AAAATGGTTTTC-AAGTTTGGT-AAT-TAACTTTGAA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG-A
8750 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT-A
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
*
8785 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
8821 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTGA
8857 AAAATGAT
1 AAAATGAT
8865 AATGAGATAA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
34 11 0.11
35 45 0.44
36 18 0.18
37 28 0.27
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:8823 original size:72 final size:69
Alignment explanation
Indices: 8716--8862 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 69
8706 TGAAAGTATT
8716 AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
1 AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
*
8780 CTTTA
65 CTTGA
** * *
8785 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGT
1 AAAATGGTTTTC-AAGTTTGGT-AAT-TAACTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGT
*
8850 TTGTTGA
63 TTCTTGA
8857 AAAATG
1 AAAATG
8863 ATAATGAGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 12 0.18
70 9 0.13
71 3 0.04
72 43 0.63
73 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTTC
TTGA
Found at i:9264 original size:12 final size:12
Alignment explanation
Indices: 9247--9281 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
9237 TTTTTTGCGA
9247 GGTTACTATTCG
1 GGTTACTATTCG
9259 GGTTACTATTCG
1 GGTTACTATTCG
9271 GGTTACTATTC
1 GGTTACTATTC
9282 ACGTGAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (12 bp):
GGTTACTATTCG
Found at i:9304 original size:16 final size:17
Alignment explanation
Indices: 9283--9314 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9273 TTACTATTCA
9283 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
9299 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
9315 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:13385 original size:21 final size:21
Alignment explanation
Indices: 13361--13421 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
13351 AACTTTGAAA
13361 AAATGATTTTCAAAGTTTGGT
1 AAATGATTTTCAAAGTTTGGT
*
13382 AAATG--TTTC----TTT-GA
1 AAATGATTTTCAAAGTTTGGT
13396 AAATGATTTTCAAAGTTTGGT
1 AAATGATTTTCAAAGTTTGGT
13417 AAATG
1 AAATG
13422 TTTCCTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 4 0.13
19 4 0.13
20 3 0.10
21 11 0.35
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (21 bp):
AAATGATTTTCAAAGTTTGGT
Found at i:13448 original size:36 final size:36
Alignment explanation
Indices: 13359--13473 Score: 164
Period size: 35 Copynumber: 3.2 Consensus size: 36
13349 CCAACTTTGA
*
13359 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
13395 -AAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
* * *
13430 AAAAATAGTTTTTC-AAGTTTGGTAGATGTTT-GTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCCTTG
13465 AAAAATGAT
1 AAAAATGAT
13474 AATGGGATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 2 0.03
35 43 0.60
36 21 0.29
37 6 0.08
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
Found at i:18090 original size:36 final size:36
Alignment explanation
Indices: 17976--18097 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
17966 TGGTAACCAA
17976 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
18013 CTTTG-AAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
18048 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
18085 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
18098 AATGGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:26608 original size:36 final size:36
Alignment explanation
Indices: 26568--26659 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
26558 ATTGCCGCTG
* *
26568 ATCTCTCGTACACGATCAATATCACCATTGTTGTCA
1 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
26604 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
1 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
26640 ATCTCTCGTTCACAATCAAT
1 ATCTCTCGTTCACAATCAAT
26660 GCGCTTTTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (36 bp):
ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
Found at i:28299 original size:17 final size:17
Alignment explanation
Indices: 28277--28315 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
28267 AAATATTCAC
28277 AAATAATCAAGTTCAAT
1 AAATAATCAAGTTCAAT
28294 AAATAATCAAGTTCAAT
1 AAATAATCAAGTTCAAT
28311 AAATA
1 AAATA
28316 TTCACAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (17 bp):
AAATAATCAAGTTCAAT
Found at i:35661 original size:21 final size:25
Alignment explanation
Indices: 35637--35681 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 25
35627 ATTATCCAGC
35637 TGATA-AT-CAAAA-ATT-AATTAG
1 TGATATATACAAAATATTCAATTAG
35658 TGATATATACAAAATATTCAATTA
1 TGATATATACAAAATATTCAATTA
35682 TTATTAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (25 bp):
TGATATATACAAAATATTCAATTAG
Found at i:35947 original size:17 final size:16
Alignment explanation
Indices: 35921--35972 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
35911 TATTTAGGGA
35921 TAATTGTTATAATATTT
1 TAATTGTTAT-ATATTT
* *
35938 TAATTTTTATATTTTT
1 TAATTGTTATATATTT
35954 TAATTAAGTTAT-TATTT
1 TAATT--GTTATATATTT
35971 TA
1 TA
35973 TCGAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 10 0.34
17 15 0.52
18 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TAATTGTTATATATTT
Found at i:40216 original size:16 final size:16
Alignment explanation
Indices: 40197--40227 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40187 AATTGAATTA
*
40197 TATTTAAATTATTTGT
1 TATTGAAATTATTTGT
40213 TATTGAAATTATTTG
1 TATTGAAATTATTTG
40228 AGTATCGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
TATTGAAATTATTTGT
Found at i:42129 original size:191 final size:191
Alignment explanation
Indices: 41804--42178 Score: 662
Period size: 191 Copynumber: 2.0 Consensus size: 191
41794 TTTGACTATC
41804 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
1 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
* *
41869 TAATATTTAACGAAATATGTGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATTCT
66 TAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCCT
*
41934 AGTACTTATATATTATTTTAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
131 AGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
* * *
41995 GATGTTTTAATTTGATCAATCATATCACTCAACTATTTATAT-GTTTCAATCAAGCCACATGTCA
1 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTT-AATCAAGCCACATGTCA
* *
42059 TTAATATTTAACGGAGTATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCC
65 TTAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCC
42124 TAGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATT
130 TAGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATT
42179 TAATAATCAA
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
190 4 0.02
191 171 0.98
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (191 bp):
GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
TAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCCT
AGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
Found at i:42188 original size:18 final size:20
Alignment explanation
Indices: 42155--42194 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
42145 ATTTGGTCAT
42155 AATTGTAATAAATCAAAATA
1 AATTGTAATAAATCAAAATA
*
42175 AATT-TAAT-AATCAAATTA
1 AATTGTAATAAATCAAAATA
42193 AA
1 AA
42195 AGGTGCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AATTGTAATAAATCAAAATA
Found at i:42487 original size:16 final size:16
Alignment explanation
Indices: 42451--42496 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
42441 TATTATCATC
42451 ACTTAAAATATATTT-
1 ACTTAAAATATATTTA
42466 --TTAAAA-ATATCTTA
1 ACTTAAAATATAT-TTA
42480 ACTTAAAATATATTTA
1 ACTTAAAATATATTTA
42496 A
1 A
42497 ATATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.15
13 8 0.31
16 10 0.38
17 4 0.15
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
ACTTAAAATATATTTA
Found at i:42784 original size:89 final size:88
Alignment explanation
Indices: 42621--42830 Score: 205
Period size: 89 Copynumber: 2.4 Consensus size: 88
42611 ACATATTAAA
* * ** *
42621 ATATTTTTAATTTAAAATAAGAATAAAATATA-TCTTAACTTCAAAATATATTTTAATATATTCT
1 ATATTTTTAATTT-AAATAAGAATAAAATATATTCTTAACGTCAAAATATAGTAAAATATATTAT
*
42685 TAAAAGTTAAAGATAATA-ATAAATT
65 TAAAAGTTAAA-ATAA-ACATAAAAT
* *
42710 ATATTTTTAATTTGAAATAAGAATAAAATATATTTTTAA-GTGAAAATAATAGTAAAATATA-TA
1 ATATTTTTAATTT-AAATAAGAATAAAATATATTCTTAACGTCAAAAT-ATAGTAAAATATATTA
*
42773 TTATATA-TTAAAATAAACATAAAAT
64 TTA-AAAGTTAAAATAAACATAAAAT
* * * *
42798 ATATTTGTTAAGTTAAACAAAAATAAAAGATAT
1 ATATTT-TTAATTTAAATAAGAATAAAATATAT
42831 ATAAAATATT
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
87 1 0.01
88 32 0.31
89 52 0.51
90 17 0.17
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (88 bp):
ATATTTTTAATTTAAATAAGAATAAAATATATTCTTAACGTCAAAATATAGTAAAATATATTATT
AAAAGTTAAAATAAACATAAAAT
Found at i:42814 original size:30 final size:29
Alignment explanation
Indices: 42621--42830 Score: 153
Period size: 29 Copynumber: 7.1 Consensus size: 29
42611 ACATATTAAA
* *
42621 ATATTTTTAATTTAAAATAAGAATAAAAT
1 ATATTTTTAAGTTAAAATAATAATAAAAT
* * * **
42650 ATA-TCTTAACTTCAAAAT-ATATTTTAAT
1 ATATTTTTAAGTT-AAAATAATAATAAAAT
* *
42678 ATATTCTTAAAAGTTAAAGATAATAATAAATT
1 ATATT-TT-TAAGTTAAA-ATAATAATAAAAT
* * *
42710 ATATTTTTAATTTGAAATAAGAATAAAAT
1 ATATTTTTAAGTTAAAATAATAATAAAAT
* *
42739 ATATTTTTAAGTGAAAATAATAGTAAAAT
1 ATATTTTTAAGTTAAAATAATAATAAAAT
*
42768 ATATATTATATA-TTAAAATAA-ACATAAAAT
1 ATAT-TTTTA-AGTTAAAATAATA-ATAAAAT
*
42798 ATATTTGTTAAGTTAAACA-AA-AATAAAAG
1 ATATTT-TTAAGTTAAA-ATAATAATAAAAT
42827 ATAT
1 ATAT
42831 ATAAAATATT
Statistics
Matches: 141, Mismatches: 28, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
28 16 0.11
29 62 0.44
30 42 0.30
31 10 0.07
32 11 0.08
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (29 bp):
ATATTTTTAAGTTAAAATAATAATAAAAT
Found at i:42825 original size:59 final size:59
Alignment explanation
Indices: 42724--42841 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
42714 TTTTAATTTG
* * * *
42724 AAATAAGAATAAAATATATTTTTAAGTGAAAATAATAGTAAAATATATATTATATATTA
1 AAATAAGAATAAAATATATTTTTAAGTGAAAATAATAATAAAAGATATATAAAATATTA
*
42783 AAATAA-ACATAAAATATATTTGTTAAGTTAAACA-AA-AATAAAAGATATATAAAATATTA
1 AAATAAGA-ATAAAATATATTT-TTAAGTGAAA-ATAATAATAAAAGATATATAAAATATTA
42842 TTAATTTTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 1 0.02
59 38 0.75
60 11 0.22
61 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (59 bp):
AAATAAGAATAAAATATATTTTTAAGTGAAAATAATAATAAAAGATATATAAAATATTA
Found at i:45842 original size:13 final size:13
Alignment explanation
Indices: 45821--45875 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45811 AAGTTCGATA
*
45821 AATTCAAATACTT
1 AATTGAAATACTT
45834 AATTGAAATACTT
1 AATTGAAATACTT
* *
45847 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
45861 AATTGAAATACTT
1 AATTGAAATACTT
45874 AA
1 AA
45876 ATACTTCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:45906 original size:33 final size:32
Alignment explanation
Indices: 45861--45926 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
45851 AACTCAACAT
* * *
45861 AATTGAAATACTTAAATACTTCTAAGTTTGATA
1 AATTCAAATACTTAAAAACTTC-AAGTTCGATA
45894 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
45926 A
1 A
45927 TTGAAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:45945 original size:21 final size:21
Alignment explanation
Indices: 45921--45983 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
45911 ACTTCAAGTT
45921 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
45942 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
* *
45963 CGAGAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
45984 AAAATAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:48241 original size:14 final size:15
Alignment explanation
Indices: 48222--48254 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48212 TAAAAACCGG
*
48222 TTTTTT-AACCGGTT
1 TTTTTTAAACCGATT
48236 TTTTTTAAACCGATT
1 TTTTTTAAACCGATT
48251 TTTT
1 TTTT
48255 ATCCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (15 bp):
TTTTTTAAACCGATT
Found at i:53751 original size:16 final size:17
Alignment explanation
Indices: 53732--53769 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53722 TTATCAATAG
53732 AAAATATA-AAAAATCT
1 AAAATATACAAAAATCT
* *
53748 AAAATATACAATAATTT
1 AAAATATACAAAAATCT
53765 AAAAT
1 AAAAT
53770 TTTAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATACAAAAATCT
Found at i:53900 original size:25 final size:25
Alignment explanation
Indices: 53847--53900 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
53837 TTTACTATGC
* *
53847 TTTTAGTTTATATAATTACTCTAAT
1 TTTTAGTTTATATAATTAATCTAAA
*
53872 TTTTAGTTTATATAA-TAATTTAAAA
1 TTTTAGTTTATATAATTAATCT-AAA
53897 TTTT
1 TTTT
53901 TAGAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTAGTTTATATAATTAATCTAAA
Found at i:59879 original size:16 final size:16
Alignment explanation
Indices: 59858--59902 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 16
59848 TCTCTAAAAA
59858 ATTTAAATTTTTTTAT
1 ATTTAAATTTTTTTAT
59874 ATTT-AATTTTTTT-T
1 ATTTAAATTTTTTTAT
59888 A--TAAATTTTTTTAT
1 ATTTAAATTTTTTTAT
59902 A
1 A
59903 ATTATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 9 0.33
14 4 0.15
15 9 0.33
16 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTAAATTTTTTTAT
Found at i:59909 original size:14 final size:14
Alignment explanation
Indices: 59864--59909 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
59854 AAAAATTTAA
*
59864 ATTTTTTTATATTT
1 ATTTTTTTATAATT
59878 AATTTTTTTTATAA--
1 -A-TTTTTTTATAATT
59892 ATTTTTTTATAATT
1 ATTTTTTTATAATT
59906 ATTT
1 ATTT
59910 AATTTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
14 4 0.15
15 1 0.04
16 10 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTTTTATAATT
Found at i:59915 original size:28 final size:28
Alignment explanation
Indices: 59861--59915 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
59851 CTAAAAAATT
* *
59861 TAAATTTTTTTATATTTAATTTTTTTTA
1 TAAATTTTTTTATAATTAATTTATTTTA
59889 TAAATTTTTTTATAATT-ATTTAATTTT
1 TAAATTTTTTTATAATTAATTT-ATTTT
59916 GTATATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (28 bp):
TAAATTTTTTTATAATTAATTTATTTTA
Found at i:72070 original size:21 final size:21
Alignment explanation
Indices: 72019--72071 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
72009 ATTATGACTA
72019 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
72040 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
72061 TCGCAATGCGA
1 TCGCAATGCGA
72072 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:72086 original size:20 final size:21
Alignment explanation
Indices: 72061--72112 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
72051 TTTTCCCAAT
*
72061 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
72081 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
72102 TCGCAATGCGA
1 TCGCAATGCGA
72113 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:72091 original size:41 final size:41
Alignment explanation
Indices: 72046--72255 Score: 140
Period size: 41 Copynumber: 5.1 Consensus size: 41
72036 AATTTCGCGT
*
72046 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
72087 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
72128 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
72169 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
72210 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
72251 TGCGA
1 TGCGA
72256 ATCTTACTAT
Statistics
Matches: 126, Mismatches: 36, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.02
40 25 0.20
41 97 0.77
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:72156 original size:21 final size:21
Alignment explanation
Indices: 72122--72194 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
72112 ATACTGACTA
* *
72122 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
72143 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
72163 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
72184 TCGCAATGCGA
1 TCGCAATGCGA
72195 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:72209 original size:20 final size:20
Alignment explanation
Indices: 72184--72275 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
72174 TTTTCATAAT
72184 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
72204 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
72224 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
72245 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
72265 TCGCAATGCGA
1 TCGCAATGCGA
72276 TTTACATAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.02
20 40 0.68
21 18 0.31
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:72245 original size:21 final size:21
Alignment explanation
Indices: 72061--72257 Score: 104
Period size: 20 Copynumber: 9.6 Consensus size: 21
72051 TTTTCCCAAT
72061 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
** *
72081 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGTAAA
* * *
72102 TCGCAATGCGATACTGACT--A
1 TCGCAATGCGA-ATTAAGTAAA
*** *
72122 TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAA-TTAAGTAAA
* * * *
72143 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAATTAAGTAAA
** * * *
72163 TCGCGTTGCGATTTTCA-TAAT
1 TCGCAATGCGA-ATTAAGTAAA
*
72184 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAAGTAAA
*
72204 TCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* *
72224 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGTAAA
72245 TCGCAATGCGAAT
1 TCGCAATGCGAAT
72258 CTTACTATCG
Statistics
Matches: 136, Mismatches: 30, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 6 0.04
20 63 0.46
21 63 0.46
22 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGTAAA
Found at i:72543 original size:27 final size:27
Alignment explanation
Indices: 72486--72538 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
72476 CATCGCCGGC
* *
72486 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
72513 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
72539 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:72904 original size:33 final size:34
Alignment explanation
Indices: 72858--72921 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
72848 CAAAATCGCA
**
72858 TTGCGATTTTCATTT-CGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
72891 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
72922 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
Found at i:72923 original size:20 final size:19
Alignment explanation
Indices: 72853--72946 Score: 81
Period size: 20 Copynumber: 5.1 Consensus size: 19
72843 GAAACCAAAA
* *
72853 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
72872 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
72888 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
72905 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
72925 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
72945 TC
1 TC
72947 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 11 0.18
16 1 0.02
17 1 0.02
19 16 0.27
20 30 0.50
21 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:75115 original size:21 final size:21
Alignment explanation
Indices: 75091--75157 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
75081 TCATTCCTCG
75091 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
75112 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
75133 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
75154 AGAG
1 AGAG
75158 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:75115 original size:42 final size:42
Alignment explanation
Indices: 75064--75157 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
75054 CCACTCATAT
* *
75064 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
75106 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
75148 CATTCAAGAG
1 CGTTCAAGAG
75158 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:76527 original size:14 final size:14
Alignment explanation
Indices: 76508--76543 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
76498 ATTGTTTAAT
76508 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
76522 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
76536 TGATTTGT
1 TGATTTGT
76544 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:76691 original size:14 final size:14
Alignment explanation
Indices: 76672--76757 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
76662 AATGAAAATT
76672 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
76686 GCAACGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
76705 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
76719 GCAACGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
76738 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
76752 CCAACG
1 GCAACG
76758 CGAAATGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 25 0.44
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 20 0.35
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.08
Consensus pattern (14 bp):
GCAACGAGAGAATC
Found at i:76695 original size:33 final size:33
Alignment explanation
Indices: 76650--76766 Score: 207
Period size: 33 Copynumber: 3.5 Consensus size: 33
76640 AAAAAGTACT
* *
76650 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
76683 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
76716 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
76749 ATCCCAACGCGAAATGAA
1 ATCGCAACGCGAAATGAA
76767 TGTATATTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:76706 original size:19 final size:19
Alignment explanation
Indices: 76650--76743 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
76640 AAAAAGTACT
*
76650 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
76669 ATTGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
76683 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
76702 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
76716 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
76735 ATCGCAACG
1 ATCGCAACG
76744 AGAGAATCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:76995 original size:113 final size:105
Alignment explanation
Indices: 76773--76998 Score: 294
Period size: 106 Copynumber: 2.1 Consensus size: 105
76763 TGAATGTATA
* *
76773 TTTTTTATTTCCGACGGAATGACTATTCTATCACAAATTAAATTGTTACATTTTAATTAAAAAAA
1 TTTTTTATTTCCGACAGAATGACTATTCCATCACAAATTAAATTGTTA-ATTTTAATTAAAAAAA
* *
76838 ATTCCGACGGAATTATTGTCCTGTCATAAATTAAATTGATT
65 ATTCCGACGGAATCATTGTCCTGTCATAAATTAAATTAATT
*
76879 TTTTTTATTTCCGACAGAATGATTATTCCATCACAAATTAAATTAGTGT-ATTTTAATTAAAGTT
1 TTTTTTATTTCCGACAGAATGACTATTCCATCACAAATTAAATT-GT-TAATTTTAATTAAA---
76943 GAACACAATTTCCGACGGAATCATTGT-CTCGTCATAAATTAAATTAATT
61 -AA-A-AA-TTCCGACGGAATCATTGTCCT-GTCATAAATTAAATTAATT
76992 TTTTTTA
1 TTTTTTA
76999 CTTAAATGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
106 53 0.50
107 2 0.02
108 1 0.01
110 2 0.02
111 1 0.01
112 4 0.04
113 42 0.40
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (105 bp):
TTTTTTATTTCCGACAGAATGACTATTCCATCACAAATTAAATTGTTAATTTTAATTAAAAAAAA
TTCCGACGGAATCATTGTCCTGTCATAAATTAAATTAATT
Found at i:80413 original size:24 final size:24
Alignment explanation
Indices: 80379--80432 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
80369 CTGAAACATC
*
80379 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
80403 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
80427 ATCAAA
1 ATCAAA
80433 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:80446 original size:24 final size:24
Alignment explanation
Indices: 80379--80446 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
80369 CTGAAACATC
* * * *
80379 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
80403 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
80427 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
80447 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:81310 original size:20 final size:20
Alignment explanation
Indices: 81263--81313 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
81253 AAGATAATAC
*
81263 AAAATCGCAACGAGATTCTG
1 AAAATCGCAATGAGATTCTG
***
81283 ACTTTCGCAATGAGATTCTG
1 AAAATCGCAATGAGATTCTG
81303 AAAATCGCAAT
1 AAAATCGCAAT
81314 CATCTTCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
AAAATCGCAATGAGATTCTG
Found at i:81574 original size:20 final size:20
Alignment explanation
Indices: 81509--81578 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
81499 ATTCATTTGA
81509 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* ** *
81529 CTATCACAATTCG-AAATGAA
1 CTATCGCAACGCGAAAATG-G
**
81549 AAATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
81569 CTATCGCAAC
1 CTATCGCAAC
81579 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:81632 original size:14 final size:14
Alignment explanation
Indices: 81613--81663 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 14
81603 AATCGCATTA
81613 CGATTTTCTCGTTG
1 CGATTTTCTCGTTG
81627 CGATTTTCATTTCGCATTG
1 CGATTTTC---TCG--TTG
81646 CGATTTTCTCGTTG
1 CGATTTTCTCGTTG
81660 CGAT
1 CGAT
81664 AGTCAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.47
16 3 0.09
17 3 0.09
19 11 0.34
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
CGATTTTCTCGTTG
Found at i:83272 original size:40 final size:42
Alignment explanation
Indices: 83228--83318 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
83218 CCTCTTCAAC
*
83228 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
83268 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
83310 AATGACAGG
1 GATGACAGG
83319 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 20 0.45
41 3 0.07
42 21 0.48
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:83298 original size:21 final size:20
Alignment explanation
Indices: 83211--83307 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
83201 TGGAATGGTG
*
83211 GGAGGGGCCTCTTCAACGAT
1 GGAGGGGCCTCTTGAACGAT
* * *
83231 GACAGTGGCCTCTTGAACGGT
1 G-GAGGGGCCTCTTGAACGAT
* **
83252 GG-GGGGACTCTTGAGGGAT
1 GGAGGGGCCTCTTGAACGAT
*
83271 GATAGGGGCCTCTTGAACGATT
1 G-GAGGGGCCTCTTGAACGA-T
*
83293 GGAGGGGACTCTTGA
1 GGAGGGGCCTCTTGA
83308 GGAATGACAG
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
19 13 0.23
20 1 0.02
21 41 0.72
22 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.23
Consensus pattern (20 bp):
GGAGGGGCCTCTTGAACGAT
Found at i:83683 original size:20 final size:20
Alignment explanation
Indices: 83658--83730 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
83648 GAAGAATAGT
*
83658 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
83678 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
83698 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
83718 TGACTATCGCAAC
1 TTACTTTCGCAAC
83731 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:83708 original size:40 final size:40
Alignment explanation
Indices: 83664--83749 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
83654 TAGTTTACTT
* *
83664 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
83704 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
83744 TCGCAA
1 TCGCAA
83750 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:83731 original size:20 final size:20
Alignment explanation
Indices: 83684--83770 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
83674 AAACTTACTT
*
83684 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
83704 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
83724 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
83744 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
83763 TCGCAACG
1 TCGCAACG
83771 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:83765 original size:19 final size:19
Alignment explanation
Indices: 83684--83825 Score: 123
Period size: 19 Copynumber: 7.6 Consensus size: 19
83674 AAACTTACTT
**
83684 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
**
83704 TCGCAACGCGGAAATGACTA
1 TCGCAACGC-GAAATGAAAA
***
83724 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
83744 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
83763 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
83777 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
83796 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
83815 TCGCAATGCGA
1 TCGCAACGCGA
83826 TTTGTGTTTC
Statistics
Matches: 107, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 45 0.42
20 45 0.42
21 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:83837 original size:19 final size:19
Alignment explanation
Indices: 83832--83897 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
83822 GCGATTTGTG
*
83832 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
83851 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
83867 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
83884 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
83898 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 19 0.49
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:83916 original size:20 final size:19
Alignment explanation
Indices: 83882--83936 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
83872 TTGCGATTTT
*
83882 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
83901 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
83921 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
83937 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:84500 original size:18 final size:18
Alignment explanation
Indices: 84477--84524 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
84467 CGGGTCGATT
84477 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
84495 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
84513 AGGTGATGGCTC
1 AGGTGATGGCTC
84525 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:85869 original size:20 final size:20
Alignment explanation
Indices: 85844--85881 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
85834 AATAGTTTCT
85844 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
85864 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
85882 GCGGATTTGA
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:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:86192 original size:22 final size:22
Alignment explanation
Indices: 86165--86208 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
86155 GATGGAGATA
86165 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
86187 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
86209 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:86426 original size:20 final size:20
Alignment explanation
Indices: 86401--86467 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
86391 GTATTATCTT
*
86401 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
86421 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
86441 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
86461 GTTGCGA
1 GTTGCGA
86468 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:86494 original size:41 final size:41
Alignment explanation
Indices: 86375--86512 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
86365 CGCTTTGAAA
* * **
86375 ATCGCATTGCGATTATGTATTATCTTGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAGT
* * ** * *
86416 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAGT
* *
86456 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAGT
*
86497 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
86513 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGAGTTGCGAAAGTCAGT
Found at i:86504 original size:20 final size:20
Alignment explanation
Indices: 86401--86509 Score: 94
Period size: 20 Copynumber: 5.4 Consensus size: 20
86391 GTATTATCTT
* * *
86401 GTTGCGAAAGTCAGTATTGA
1 GTTGCGATAGTCAGTATCGC
* * * *
86421 GTTGCGAAATTAAGTATCGA
1 GTTGCGATAGTCAGTATCGC
*
86441 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGTATCGC
* *
86461 GTTGCGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAGTATCGC
*
86482 GTTGCGATAGTCAGTACCGC
1 GTTGCGATAGTCAGTATCGC
86502 GTTGCGAT
1 GTTGCGAT
86510 TTTCCAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 55 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGTATCGC
Found at i:86528 original size:41 final size:41
Alignment explanation
Indices: 86442--86572 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
86432 AAGTATCGAG
* ** * *
86442 TTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
*
86483 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
** * *
86524 TTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGT-CAGTA-TCGCGTTGCGATTTTCCAAATTCGCA
86566 TTGCGAT
1 TTGCGAT
86573 TTACTTATTC
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
41 41 0.54
42 35 0.46
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
Found at i:86584 original size:20 final size:21
Alignment explanation
Indices: 86503--86591 Score: 144
Period size: 21 Copynumber: 4.3 Consensus size: 21
86493 CAGTACCGCG
86503 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
86524 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
86545 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
86566 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
86586 TTGCGA
1 TTGCGA
86592 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 17 0.26
21 48 0.74
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:86606 original size:41 final size:42
Alignment explanation
Indices: 86503--86606 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 42
86493 CAGTACCGCG
* * * *
86503 TTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
* * * **
86545 TTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTATTCGCA
1 TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
**
86586 TTGCGAATTGGGAAAATCGCA
1 TTGCGAATTGCCAAAATCGCA
86607 ACGCGAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 27 0.50
42 27 0.50
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
Found at i:92365 original size:14 final size:14
Alignment explanation
Indices: 92348--92374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
92338 AAGATAGCAG
92348 AAAAAGAAATAATA
1 AAAAAGAAATAATA
92362 AAAAAGAAATAAT
1 AAAAAGAAATAAT
92375 TGTTGGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAGAAATAATA
Found at i:93992 original size:16 final size:16
Alignment explanation
Indices: 93971--94004 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
93961 AATACACTAC
93971 AAGTAGAACAACTTCT
1 AAGTAGAACAACTTCT
93987 AAGTAGAACAACTTCT
1 AAGTAGAACAACTTCT
94003 AA
1 AA
94005 TGACAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (16 bp):
AAGTAGAACAACTTCT
Found at i:99307 original size:5 final size:5
Alignment explanation
Indices: 99299--99324 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
99289 TATTATTATT
99299 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
99325 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:107767 original size:18 final size:18
Alignment explanation
Indices: 107744--107778 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
107734 AATAAGGAGC
*
107744 AGAAGGAATTGGTTAAAT
1 AGAAGGAATTAGTTAAAT
107762 AGAAGGAATTAGTTAAA
1 AGAAGGAATTAGTTAAA
107779 ATCAAACGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (18 bp):
AGAAGGAATTAGTTAAAT
Done.