Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000069.1 Hibiscus syriacus cultivar Beakdansim tig00000120_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: 86462
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2658 original size:14 final size:14
Alignment explanation
Indices: 2639--2665 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2629 AAGTAATTAA
2639 ATATAAACATATAT
1 ATATAAACATATAT
2653 ATATAAACATATA
1 ATATAAACATATA
2666 AAATAAATTG
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:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAACATATAT
Found at i:3280 original size:16 final size:17
Alignment explanation
Indices: 3260--3297 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3250 TGCATTTCTT
*
3260 TAATAGTAATAATAATA
1 TAATAGTAATAAGAATA
*
3277 -AATATTAATAAGAATA
1 TAATAGTAATAAGAATA
3293 TAATA
1 TAATA
3298 ATTTTCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
TAATAGTAATAAGAATA
Found at i:3483 original size:22 final size:22
Alignment explanation
Indices: 3448--3502 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
3438 TCATATATAT
*
3448 ATATATATATAATATAATATGATAA
1 ATATA-ATA-AATATAA-ATGAAAA
3473 ATA-AATAAATATAAATGAAAA
1 ATATAATAAATATAAATGAAAA
3494 ATATAATAA
1 ATATAATAA
3503 TTTTAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 3 0.11
24 1 0.04
25 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAATAAATATAAATGAAAA
Found at i:4967 original size:3 final size:3
Alignment explanation
Indices: 4959--5021 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
4949 TATTTGTTTA
* **
4959 AAT AAT AAT ATAT AAT AAT AAT AAT -TT AAT TTT AAT AAT AAT ATAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
5005 ATT ATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
5022 AAGTAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 42 0.86
4 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:5111 original size:46 final size:46
Alignment explanation
Indices: 5048--5272 Score: 279
Period size: 46 Copynumber: 4.9 Consensus size: 46
5038 AGTGTCTACA
* ** *
5048 GATGCCACAAATGAAAATGCATAAAAGTGCATTATTGACATGAAAG
1 GATGCCACAAATGAAAATACATAACGGTGCATTATCGACATGAAAG
** * * *
5094 GATGCCGTAAATAAAAATGCATAACGGTGCATTATCGGCATGAAAG
1 GATGCCACAAATGAAAATACATAACGGTGCATTATCGACATGAAAG
*
5140 GATGCCACAAATGAAAATACATAATGGTGCATTATCGACATGAAAG
1 GATGCCACAAATGAAAATACATAACGGTGCATTATCGACATGAAAG
* * ** * *
5186 GATGCGATAAATGAAAATACATGTCGGTTCATAATCGACATGAAAG
1 GATGCCACAAATGAAAATACATAACGGTGCATTATCGACATGAAAG
* * *
5232 GATGCCACAAATAAAAATACATAACGGTGTATTAACGACAT
1 GATGCCACAAATGAAAATACATAACGGTGCATTATCGACAT
5273 AAAATGTGCC
Statistics
Matches: 150, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 150 1.00
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (46 bp):
GATGCCACAAATGAAAATACATAACGGTGCATTATCGACATGAAAG
Found at i:5992 original size:19 final size:19
Alignment explanation
Indices: 5968--6005 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5958 ACGATGGGCT
*
5968 AAATAAACTAATGGATATA
1 AAATAAACAAATGGATATA
*
5987 AAATAAACAAATTGATATA
1 AAATAAACAAATGGATATA
6006 GAATGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AAATAAACAAATGGATATA
Found at i:10801 original size:13 final size:13
Alignment explanation
Indices: 10785--10819 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
10775 ATTAATTATA
10785 ATATAATAATAAT
1 ATATAATAATAAT
*
10798 ATATGATAATAAT
1 ATATAATAATAAT
10811 ATTATAATA
1 A-TATAATA
10820 CTTGTAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:15638 original size:2 final size:2
Alignment explanation
Indices: 15631--15656 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15621 TAAACAAGAG
15631 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
15657 ATCATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20493 original size:15 final size:16
Alignment explanation
Indices: 20466--20495 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20456 AATTCTACTT
20466 AATATATAATAATATA
1 AATATATAATAATATA
20482 AATATA-AATAATAT
1 AATATATAATAATAT
20496 TAAAATAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATATAATAATATA
Found at i:20759 original size:2 final size:2
Alignment explanation
Indices: 20752--20785 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20742 TAATTTAACC
20752 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
20786 ACAGTGACTA
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):
TA
Found at i:21819 original size:13 final size:13
Alignment explanation
Indices: 21803--21837 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
21793 ATTAATTATA
21803 ATATAATAATAAT
1 ATATAATAATAAT
*
21816 ATATGATAATAAT
1 ATATAATAATAAT
21829 ATTATAATA
1 A-TATAATA
21838 CTTATAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:25021 original size:25 final size:25
Alignment explanation
Indices: 24984--25038 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
24974 GAGTCGAGGG
24984 TTCTACGCCGTCCTTCGAGACAAAT
1 TTCTACGCCGTCCTTCGAGACAAAT
** *
25009 TTCTACGTGGTCCTTCGGGACAAAT
1 TTCTACGCCGTCCTTCGAGACAAAT
25034 TTCTA
1 TTCTA
25039 TTCAGTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (25 bp):
TTCTACGCCGTCCTTCGAGACAAAT
Found at i:28082 original size:2 final size:2
Alignment explanation
Indices: 28075--28101 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28065 ATTTACCTAA
28075 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
28102 ATGATAAGGA
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:29091 original size:3 final size:3
Alignment explanation
Indices: 29085--29157 Score: 78
Period size: 3 Copynumber: 23.7 Consensus size: 3
29075 TATTATTTTT
* *
29085 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TGA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
29130 TAA TAA TAA TAA TAAA TAAA TAA TAA TA
1 TAA TAA TAA TAA T-AA T-AA TAA TAA TA
29158 TATATACTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.06
3 45 0.73
4 13 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:31290 original size:10 final size:10
Alignment explanation
Indices: 31249--31310 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
31239 TCCTGGTTCA
31249 ATTTTTTCT-
1 ATTTTTTCTC
31258 -TTTTTTC-C
1 ATTTTTTCTC
*
31266 CTTTTTTC-C
1 ATTTTTTCTC
*
31275 TTTTTTTTCTC
1 -ATTTTTTCTC
31286 A-TTTTTCTC
1 ATTTTTTCTC
31295 ATTTTTTCTC
1 ATTTTTTCTC
31305 ATTTTT
1 ATTTTT
31311 CTTTTTCATC
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
8 7 0.15
9 17 0.37
10 21 0.46
11 1 0.02
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTCTC
Found at i:31290 original size:19 final size:18
Alignment explanation
Indices: 31251--31337 Score: 90
Period size: 19 Copynumber: 4.9 Consensus size: 18
31241 CTGGTTCAAT
* *
31251 TTTTTC-TTTTTTTCCCT
1 TTTTTCTTTTTTTTCTCA
31268 TTTTTCCTTTTTTTTCTCA
1 TTTTT-CTTTTTTTTCTCA
*
31287 TTTTTCTCATTTTTTCTCA
1 TTTTTCT-TTTTTTTCTCA
**
31306 TTTTTCTTTTTCATCT--
1 TTTTTCTTTTTTTTCTCA
31322 TTTTTCTTTTTTTTCT
1 TTTTTCTTTTTTTTCT
31338 TTTTCCTCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 14 0.24
17 5 0.08
18 9 0.15
19 31 0.53
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTTTTTCTCA
Found at i:31324 original size:25 final size:24
Alignment explanation
Indices: 31287--31353 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
31277 TTTTTTCTCA
31287 TTTTTCTCATTTTTTCTCATTTTTC
1 TTTTTCTC-TTTTTTCTCATTTTTC
**
31312 TTTTTCATCTTTTTTCTTTTTTTTC
1 TTTTTC-TCTTTTTTCTCATTTTTC
*
31337 TTTTTCCTCATTTTTCT
1 TTTTT-CTCTTTTTTCT
31354 TTTTTTCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 34 0.92
26 3 0.08
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTCTTTTTTCTCATTTTTC
Found at i:31325 original size:16 final size:15
Alignment explanation
Indices: 31278--31371 Score: 58
Period size: 16 Copynumber: 6.3 Consensus size: 15
31268 TTTTTCCTTT
31278 TTTTTCTCATTTTTCTC
1 TTTTTCTCA-TTTT-TC
31295 ATTTTTTCTCATTTTTC
1 --TTTTTCTCATTTTTC
31312 -TTTT-TCATCTTTT-
1 TTTTTCTCAT-TTTTC
*
31325 TTCTT-T--TTTTTC
1 TTTTTCTCATTTTTC
31337 TTTTTCCTCATTTTTC
1 TTTTT-CTCATTTTTC
*
31353 TTTTTTTCATCTTTT-
1 TTTTTCTCAT-TTTTC
31368 TTTT
1 TTTT
31372 ATTTCTTTGC
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
11 4 0.06
12 5 0.08
13 4 0.06
14 13 0.20
15 8 0.12
16 15 0.23
17 2 0.03
18 4 0.06
19 9 0.14
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTCATTTTTC
Found at i:31367 original size:9 final size:8
Alignment explanation
Indices: 31278--31368 Score: 69
Period size: 9 Copynumber: 10.6 Consensus size: 8
31268 TTTTTCCTTT
31278 TTTTTCTC
1 TTTTTCTC
31286 ATTTTTCTC
1 -TTTTTCTC
31295 ATTTTTTCTC
1 --TTTTTCTC
*
31305 ATTTT-TC
1 TTTTTCTC
31312 TTTTTCATC
1 TTTTTC-TC
31321 TTTTT-TC
1 TTTTTCTC
*
31328 TTTTTTTTC
1 -TTTTTCTC
31337 TTTTTCCTC
1 TTTTT-CTC
*
31346 ATTTTTCTT
1 -TTTTTCTC
31355 TTTTTCATC
1 TTTTTC-TC
31364 TTTTT
1 TTTTT
31369 TTTATTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
7 8 0.12
8 20 0.29
9 27 0.40
10 13 0.19
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCTC
Found at i:32533 original size:3 final size:3
Alignment explanation
Indices: 32527--32604 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
32517 TATTATTTTT
* *
32527 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TGA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
* *
32572 TAA TTA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32605 ATAAATAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 4 0.06
3 54 0.84
4 6 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:32879 original size:17 final size:17
Alignment explanation
Indices: 32857--32915 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
32847 TTGAACAAGC
32857 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
32874 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
32893 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
32910 TCTTCT
1 TCTTCT
32916 GGAAATGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:33111 original size:17 final size:17
Alignment explanation
Indices: 33089--33139 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
33079 GTTGAACAAG
33089 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
33106 TTCTTCTTCA-GATG-AG
1 TTCTTC-TCATTATGAAC
33122 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
33139 T
1 T
33140 CTTTCACTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.11
16 10 0.37
17 11 0.41
18 3 0.11
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.47
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:33142 original size:16 final size:16
Alignment explanation
Indices: 33090--33142 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
33080 TTGAACAAGT
33090 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* **
33106 TTCTTCTTCA-GATGAGT
1 -TCTTC-TCATTATGAAC
33123 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
33139 TCTT
1 TCTT
33143 TCACTGGGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 3 0.11
16 13 0.46
17 9 0.32
18 3 0.11
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:33285 original size:221 final size:223
Alignment explanation
Indices: 32960--33372 Score: 607
Period size: 221 Copynumber: 1.8 Consensus size: 223
32950 TAGAGTCATG
* * *
32960 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTCGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
* * * * *
33025 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAA-GTTGAACAAG
66 TTATGAACTCTCTCTAGAAAAGCTGATCCATCAAGTGATGAATTCAAAC-AAAAGGTTGAACAAG
33089 TTCTTCTCATTATGAA-CTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGG
130 TTCTTCTCATTATGAATCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGG
33152 AAGCTGATCCATCAAATGATGAATTCAAA
195 AAGCTGATCCATCAAATGATGAATTCAAA
* *
33181 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
1 CAAAAGGTCGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
* * * * *
33246 TTATGAACTTTTTCTAGAAAAGCTGATCTATCAAGTGATGAATTCAAACAAAAGGTTGATCAATT
66 TTATGAACTCTCTCTAGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
*
33311 TCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
131 TCTTCTCATTATGAA-----TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC
33373 TTCTTTCTTT
Statistics
Matches: 168, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
220 4 0.02
221 125 0.74
227 3 0.02
228 36 0.21
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (223 bp):
CAAAAGGTCGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
TTATGAACTCTCTCTAGAAAAGCTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
TCTTCTCATTATGAATCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGGA
AGCTGATCCATCAAATGATGAATTCAAA
Found at i:33368 original size:113 final size:113
Alignment explanation
Indices: 32960--33373 Score: 547
Period size: 113 Copynumber: 3.7 Consensus size: 113
32950 TAGAGTCATG
* ** *
32960 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
33025 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAG
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
*
33073 CGAAAA-GTTGAACAAGTTCTTCTCATTATGAA------CTT-CTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** *
33130 ATTATGAACTCTTTCACTGGGGAAGCTGATCCATCAAATGATGAATTCAAA
65 ATTATGAACT-TTT-TCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
*
33181 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
33246 TTATGAACTTTTTCTAGAAAAGCTGATCTATCAAGTGATGAATTCAAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
* * * *
33294 CAAAAGGTTGATCAATTTCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
33359 TTATGAACTTTTTCT
66 TTATGAACTTTTTCT
33374 TCTTTCTTTA
Statistics
Matches: 264, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
106 31 0.12
107 8 0.03
108 54 0.20
113 130 0.49
114 10 0.04
115 31 0.12
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAAA
Found at i:33410 original size:40 final size:40
Alignment explanation
Indices: 33310--33411 Score: 161
Period size: 40 Copynumber: 2.5 Consensus size: 40
33300 GTTGATCAAT
*
33310 TTCTTCTCATTATGAA-TTTCCTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAG
* *
33350 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTTAGATGAG
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
33390 TTCTTCTCATTATGAACTTTTT
1 TTCTTCTCATTATGAACTTTTT
33412 TCTGGAAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 55 0.95
41 3 0.05
ACGTcount: A:0.18, C:0.21, G:0.09, T:0.53
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
Found at i:33464 original size:267 final size:267
Alignment explanation
Indices: 33087--33644 Score: 824
Period size: 267 Copynumber: 2.1 Consensus size: 267
33077 AAGTTGAACA
33087 AGTTCTTCTCATTATGAAC---TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTG
1 AGTTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTG
**
33149 GGGAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
33214 TTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTAGAAAAGCTGAT-C-T-A
131 TTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTAGAAAAGCTGATGCATCA
* * *
33276 TCAAGTGATGAATTCAAACAAAAGGTTGATCAATTTCTTCTCATTATGAATTTCCTCTTCCTTCT
196 TCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTCT
33341 TCAGATG
261 TCAGATG
*
33348 AGTTCTTCTCATTATGAACTTTTTCTTCTTTCTTTAGATGAGTTCTTCTCATTATGAACT-TTTT
1 AGTTCTTCTCATTATGAACTTTTTCTTC-TTC---AGATGAGTTCTTCTCATTATGAACTCTTTC
* * ** *
33412 TCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTAT
62 ACTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTAT
* * * *
33477 GAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATGC
127 GAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTAGAAAAGCTGATGC
* ** * *
33542 TGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
192 --AT-CATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCT
33607 TCCTTCTTCAGATG
254 TCCTTCTTCAGATG
33621 AGTTCTTCTCATTATGAACTTTTT
1 AGTTCTTCTCATTATGAACTTTTT
33645 TCTGGAAAAG
Statistics
Matches: 264, Mismatches: 20, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
261 19 0.07
264 6 0.02
265 3 0.01
267 120 0.45
268 26 0.10
271 1 0.00
273 89 0.34
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (267 bp):
AGTTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTG
GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTAGAAAAGCTGATGCATCA
TCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTCT
TCAGATG
Found at i:33481 original size:154 final size:153
Alignment explanation
Indices: 33197--33527 Score: 518
Period size: 154 Copynumber: 2.2 Consensus size: 153
33187 GTTGAACAAA
*
33197 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTA
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTA
* * * *
33262 GAAAAGCTGATCTATCAAGTGATGAATTCAAACAAAAGGTTGATCAATTTCTTCTCATTATGAAT
66 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
33327 TTCCTCTTCCTTCTTCAGATGAG
131 TTCCTCTTCCTTCTTCAGATGAG
* * *
33350 TTCTTCTCATTATGAACTTTTTCTTCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAAC-TTTTTCT
* * ** *
33415 GGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
65 AGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
* *
33480 TTTCTTCTTCCTTCTTTAGATGAG
130 TTTCCTCTTCCTTCTTCAGATGAG
33504 TTCTTCTCATTATGAACTTTTTCT
1 TTCTTCTCATTATGAACTTTTTCT
33528 GGAAAAGCTG
Statistics
Matches: 162, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
153 53 0.33
154 109 0.67
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (153 bp):
TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTCCTTCTCATTATGAACTTTTTCTA
GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAT
TTCCTCTTCCTTCTTCAGATGAG
Found at i:33593 original size:119 final size:120
Alignment explanation
Indices: 33350--33765 Score: 553
Period size: 119 Copynumber: 3.5 Consensus size: 120
33340 TTCAGATGAG
* *
33350 TTCTTCTCATTATGAACTTT-TTCTTCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTTC
1 TTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTC
33414 TGG-AAA----A-GCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
65 TGGAAAAGCTGATGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
33464 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAAC-TTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
33528 GGAAAAGCTGATGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GGAAAAGCTGATGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
33583 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
** ** *** ** * *
33648 GGAAAAGCTGATAATGATATATCTCCTTCTGTGATATAATCTAGCAAAAGGTTGAACGAA
66 GGAAAAGCTGATGCTGATCCATCAAATGATG-GAT-T--T-GAGCAAAAGGTTGAACAAA
* * * *
33708 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGCTCTCCTCATTATAAACTT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
33766 CATATGGAAA
Statistics
Matches: 272, Mismatches: 17, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
113 12 0.04
114 55 0.20
118 1 0.00
119 99 0.36
120 29 0.11
121 3 0.01
122 1 0.00
124 29 0.11
125 43 0.16
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (120 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
GGAAAAGCTGATGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:35914 original size:78 final size:78
Alignment explanation
Indices: 35785--35948 Score: 328
Period size: 78 Copynumber: 2.1 Consensus size: 78
35775 GTTACTCCTC
35785 ATCCATCTCGTGCGTGACCATAAACTCTACACTTGAAACAGATACGTTGAAGTCCTTCATATTCC
1 ATCCATCTCGTGCGTGACCATAAACTCTACACTTGAAACAGATACGTTGAAGTCCTTCATATTCC
35850 AATTGTTGTATGA
66 AATTGTTGTATGA
35863 ATCCATCTCGTGCGTGACCATAAACTCTACACTTGAAACAGATACGTTGAAGTCCTTCATATTCC
1 ATCCATCTCGTGCGTGACCATAAACTCTACACTTGAAACAGATACGTTGAAGTCCTTCATATTCC
35928 AATTGTTGTATGA
66 AATTGTTGTATGA
35941 ATCCATCT
1 ATCCATCT
35949 ATTCCAATGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 86 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (78 bp):
ATCCATCTCGTGCGTGACCATAAACTCTACACTTGAAACAGATACGTTGAAGTCCTTCATATTCC
AATTGTTGTATGA
Found at i:40598 original size:13 final size:13
Alignment explanation
Indices: 40577--40628 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
40567 AATGACACGC
40577 AATGCGCGTCATA
1 AATGCGCGTCATA
*
40590 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
40603 AATGTGTGTCATA
1 AATGCGCGTCATA
40616 AATGCGCGTCATA
1 AATGCGCGTCATA
40629 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:42647 original size:20 final size:19
Alignment explanation
Indices: 42605--42654 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
42595 TGGGCTAGAA
42605 GTATCGATATTGTAGGTGAG
1 GTATCGATATTGTAGGT-AG
42625 GTATCGATATTCGTAGG-ATG
1 GTATCGATATT-GTAGGTA-G
*
42645 GTATCAATAT
1 GTATCGATAT
42655 CGAGTTCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 21 0.78
21 5 0.19
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (19 bp):
GTATCGATATTGTAGGTAG
Found at i:43664 original size:7 final size:7
Alignment explanation
Indices: 43652--43676 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43642 GTAAACTTTG
43652 AATTATT
1 AATTATT
43659 AATTATT
1 AATTATT
43666 AATTATT
1 AATTATT
43673 AATT
1 AATT
43677 TTATTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:47164 original size:17 final size:17
Alignment explanation
Indices: 47142--47176 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47132 ATGTAAAATC
47142 AAATTATGATTTAATAT
1 AAATTATGATTTAATAT
* *
47159 AAATTATTATTTATTAT
1 AAATTATGATTTAATAT
47176 A
1 A
47177 TATATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTATGATTTAATAT
Found at i:48500 original size:9 final size:9
Alignment explanation
Indices: 48460--48523 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
48450 TTGGGTTTTG
48460 TAAT-ATTA
1 TAATAATTA
48468 -AATAATATA
1 TAATAAT-TA
* *
48477 TATTAATAA
1 TAATAATTA
48486 TAATAATTA
1 TAATAATTA
*
48495 TTATAATTA
1 TAATAATTA
* *
48504 TAATTATAA
1 TAATAATTA
*
48513 TAATTATTA
1 TAATAATTA
48522 TA
1 TA
48524 TAAATAACAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
7 3 0.07
8 2 0.05
9 34 0.77
10 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATAATTA
Found at i:48530 original size:15 final size:15
Alignment explanation
Indices: 48480--48519 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
48470 TAATATATAT
*
48480 TAATAATAATAATTA
1 TAATAATTATAATTA
*
48495 TTATAATTATAATTA
1 TAATAATTATAATTA
48510 TAATAATTAT
1 TAATAATTAT
48520 TATATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAATTATAATTA
Found at i:50018 original size:19 final size:19
Alignment explanation
Indices: 49979--50026 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
49969 TTCATAATTT
49979 ATTTTTGAAATTATAAATAA
1 ATTTTT-AAATTATAAATAA
**
49999 ATTTTTAAATTATATTTAA
1 ATTTTTAAATTATAAATAA
50018 ATTTATTAA
1 ATTT-TTAA
50027 CTAGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTTAAATTATAAATAA
Found at i:50380 original size:18 final size:19
Alignment explanation
Indices: 50347--50382 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50337 TATTTATTAA
*
50347 TTAATTTTTCTTGTTTTAT
1 TTAATTTTTCTAGTTTTAT
50366 TTAATTTTT-TAGTTTTA
1 TTAATTTTTCTAGTTTTA
50383 CTAACTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (19 bp):
TTAATTTTTCTAGTTTTAT
Found at i:51852 original size:31 final size:29
Alignment explanation
Indices: 51772--51853 Score: 71
Period size: 31 Copynumber: 2.7 Consensus size: 29
51762 ATAGTAACAA
51772 AAAACATAATAA-AA-AATAAAAAAAGAAT
1 AAAA-ATAATAATAATAATAAAAAAAGAAT
**
51800 AAAAAT-ATATATATATAAATAAAAAATATTAT
1 AAAAATAATA-ATA-AT-AATAAAAAA-AGAAT
51832 AAAGAATAATAATAATAATAAA
1 AAA-AATAATAATAATAATAAA
51854 CAGAAACAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 5 0.11
29 1 0.02
31 15 0.34
32 8 0.18
33 6 0.14
34 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (29 bp):
AAAAATAATAATAATAATAAAAAAAGAAT
Found at i:51917 original size:4 final size:4
Alignment explanation
Indices: 51903--51932 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
51893 ATATTAATGT
51903 TAAA TTAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA T
51933 GTGGAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:54806 original size:6 final size:6
Alignment explanation
Indices: 54797--54839 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
54787 ATTTTTATTT
54797 TTTTTC TTTTTC TTTTTTC TTTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTT
54840 TCAATTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:54806 original size:7 final size:7
Alignment explanation
Indices: 54796--54841 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
54786 TATTTTTATT
54796 TTTTTTC
1 TTTTTTC
54803 -TTTTTC
1 TTTTTTC
54809 TTTTTTC
1 TTTTTTC
54816 TTTTTTC
1 TTTTTTC
54823 -TTTTTC
1 TTTTTTC
54829 -TTTTTC
1 TTTTTTC
54835 TTTTTTC
1 TTTTTTC
54842 AATTTAGGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.49
7 19 0.51
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:54814 original size:13 final size:13
Alignment explanation
Indices: 54796--54841 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
54786 TATTTTTATT
54796 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
54809 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
54821 TCTTTTTCTTTTTC
1 T-TTTTTCTTTTTC
54835 TTTTTTC
1 TTTTTTC
54842 AATTTAGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.03
13 29 0.94
14 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:62372 original size:151 final size:152
Alignment explanation
Indices: 62090--62391 Score: 597
Period size: 151 Copynumber: 2.0 Consensus size: 152
62080 CCATAATGGA
62090 TTCTAACTCAACAATGGTATTTTCATCCCGTTCTTTTTGTTTCTGAAGATACTTCTCTAATTTGG
1 TTCTAACTCAACAATGGTATTTTCATCCCGTTCTTTTTGTTTCTGAAGATACTTCTCTAATTTGG
62155 ATACTTAGATTCTCAAAAGATTATAGTAATGCTGGCTGTTTATCAAACGCATCTGAGCAGTCCTT
66 ATACTTAGATTCTCAAAAGATTATAGTAATGCTGGCTGTTTATCAAACGCATCTGAGCAGTCCTT
62220 AGCTGTTCTTTCAGAGTCTCTT
131 AGCTGTTCTTTCAGAGTCTCTT
62242 TTCTAAC-CAACAATGGTATTTTCATCCCGTTCTTTTTGTTTCTGAAGATACTTCTCTAATTTGG
1 TTCTAACTCAACAATGGTATTTTCATCCCGTTCTTTTTGTTTCTGAAGATACTTCTCTAATTTGG
62306 ATACTTAGATTCTCAAAAGATTATAGTAATGCTGGCTGTTTATCAAACGCATCTGAGCAGTCCTT
66 ATACTTAGATTCTCAAAAGATTATAGTAATGCTGGCTGTTTATCAAACGCATCTGAGCAGTCCTT
62371 AGCTGTTCTTTCAGAGTCTCT
131 AGCTGTTCTTTCAGAGTCTCT
62392 CTTTTATCAT
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 143 0.95
152 7 0.05
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (152 bp):
TTCTAACTCAACAATGGTATTTTCATCCCGTTCTTTTTGTTTCTGAAGATACTTCTCTAATTTGG
ATACTTAGATTCTCAAAAGATTATAGTAATGCTGGCTGTTTATCAAACGCATCTGAGCAGTCCTT
AGCTGTTCTTTCAGAGTCTCTT
Found at i:65555 original size:19 final size:20
Alignment explanation
Indices: 65521--65567 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
65511 AAAGAAGGGA
* *
65521 AATAATAATAATAAAATATAT
1 AATAA-AATAACAAAAAATAT
65542 AA-AAAATAACAAAAAATAT
1 AATAAAATAACAAAAAATAT
65561 AATAAAA
1 AATAAAA
65568 AATGAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AATAAAATAACAAAAAATAT
Found at i:65565 original size:22 final size:22
Alignment explanation
Indices: 65524--65570 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
65514 GAAGGGAAAT
*
65524 AATAATAATAAAATATATAAAA
1 AATAACAATAAAATATATAAAA
65546 AATAACAA-AAAATATAATAAAA
1 AATAACAATAAAATAT-ATAAAA
65568 AAT
1 AAT
65571 GAATAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AATAACAATAAAATATATAAAA
Found at i:65575 original size:11 final size:10
Alignment explanation
Indices: 65524--65576 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 10
65514 GAAGGGAAAT
65524 AATAATAATAA
1 AATAATAA-AA
65535 AATATATAAAA
1 AATA-ATAAAA
*
65546 AATAACAAAAA
1 AATAA-TAAAA
65557 ATATAATAAAA
1 A-ATAATAAAA
65568 AATGAATAA
1 AAT-AATAA
65577 GAATAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 3 0.08
11 25 0.69
12 8 0.22
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
AATAATAAAA
Found at i:71950 original size:74 final size:74
Alignment explanation
Indices: 71770--72220 Score: 466
Period size: 74 Copynumber: 6.1 Consensus size: 74
71760 TGAAGCGGAG
* * * *
71770 GATG-TTACCTGACCAATATGATGCTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTTCC
1 GATGATTACCTGACCAATAAGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGA-TTTTCA
*
71834 AAGGTTTTTT
65 AAGGTTTCTT
* *** *
71844 GATGACTA-CTCGATTGATACA-ATGTTTCCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTC
1 GATGATTACCT-GACCAATA-AGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTC
**
71907 AAATGG-TTCAC
64 AAA-GGTTTCTT
* * * *
71918 GATGATTACCCGACCAATAAGATGTTTTCAAATTATTTTTTAAAGAAACCAAGTTTGATTTTTAA
1 GATGATTACCTGACCAATAAGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTCAA
71983 AGGTTTCTT
66 AGGTTTCTT
*** * * ** * *
71992 GATGATTATAGGACCGATACGATGTTTTCAAAT-AAATTTTAAAGAAGACAAATTTGATTTTCAA
1 GATGATTACCTGACCAATAAGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTCAA
72056 AGGTTTCTT
66 AGGTTTCTT
* * * * * *
72065 GATGATTACCTAACCAATATGATGTTTTCAAATGAATTTTTAAAGAACCCAAGTTTAATTTTCAA
1 GATGATTACCTGACCAATAAGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTCAA
72130 AGGTTTCTT
66 AGGTTTCTT
* * * * * *
72139 GATGATTACCTGATCGATATA-ATGCTTTCAAATAAATTTTTGAAA-AAGACAAGTTTGATTTTC
1 GATGATTACCTGACCAATA-AGATGTTTTCAAAT-CATTTTTTAAAGAAGCCAAGTTTGATTTTC
72202 AAAGGTTTCTT
64 AAAGGTTTCTT
72213 GATGATTA
1 GATGATTA
72221 AATCATTCGG
Statistics
Matches: 311, Mismatches: 56, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
73 64 0.21
74 195 0.63
75 52 0.17
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (74 bp):
GATGATTACCTGACCAATAAGATGTTTTCAAATCATTTTTTAAAGAAGCCAAGTTTGATTTTCAA
AGGTTTCTT
Found at i:72089 original size:147 final size:146
Alignment explanation
Indices: 71770--72220 Score: 566
Period size: 147 Copynumber: 3.1 Consensus size: 146
71760 TGAAGCGGAG
* *
71770 GATG-TTACCTGACCAATATGATGCTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTTCC
1 GATGATTACCTGACCAATATGATGTTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTT-A
* * * * ** *
71834 AAGGTTTTTTGATGACTACTCGATTGATACAATGTTTCCAAATCATTTTTTAAAGAAGCCAAGTT
65 AAGGTTTCTTGATGATTA-TCGATCGATACAATGTTTTCAAAT-AAATTTTAAAGAAGACAAGTT
**
71899 TGATTTTCAAATGG-TTCAC
128 TGATTTTCAAA-GGTTTCTT
* * * *
71918 GATGATTACCCGACCAATAAGATGTTTTCAAATTATTTTTTAAAGAAACCAAGTTTGATTTTTAA
1 GATGATTACCTGACCAATATGATGTTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTTAA
* * * *
71983 AGGTTTCTTGATGATTATAGGACCGATACGATGTTTTCAAATAAATTTTAAAGAAGACAAATTTG
66 AGGTTTCTTGATGATTAT-CGATCGATACAATGTTTTCAAATAAATTTTAAAGAAGACAAGTTTG
72048 ATTTTCAAAGGTTTCTT
130 ATTTTCAAAGGTTTCTT
* * * * *
72065 GATGATTACCTAACCAATATGATGTTTTCAAATGAATTTTTAAAGAACCCAAGTTTAATTTTCAA
1 GATGATTACCTGACCAATATGATGTTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTTAA
* * *
72130 AGGTTTCTTGATGATTACCTGATCGATATAATGCTTTCAAATAAATTTTTGAAA-AAGACAAGTT
66 AGGTTTCTTGATGATTATC-GATCGATACAATGTTTTCAAATAAA-TTTT-AAAGAAGACAAGTT
72194 TGATTTTCAAAGGTTTCTT
128 TGATTTTCAAAGGTTTCTT
72213 GATGATTA
1 GATGATTA
72221 AATCATTCGG
Statistics
Matches: 263, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
146 2 0.01
147 127 0.48
148 78 0.30
149 56 0.21
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (146 bp):
GATGATTACCTGACCAATATGATGTTTTCAAATCATTTTTTAAAGAACCCAAGTTTGATTTTTAA
AGGTTTCTTGATGATTATCGATCGATACAATGTTTTCAAATAAATTTTAAAGAAGACAAGTTTGA
TTTTCAAAGGTTTCTT
Found at i:72269 original size:42 final size:42
Alignment explanation
Indices: 72210--72290 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
72200 TCAAAGGTTT
* *
72210 CTTGATGATTAAATCATTCGGGTCATCAGTAAGTCTTTCAAG
1 CTTGATAATTAAATCATTCGGGCCATCAGTAAGTCTTTCAAG
*
72252 CTTGATAATTAAATCATTCGGGCCATCTGTAAGTCTTTC
1 CTTGATAATTAAATCATTCGGGCCATCAGTAAGTCTTTC
72291 GAGCAGGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (42 bp):
CTTGATAATTAAATCATTCGGGCCATCAGTAAGTCTTTCAAG
Found at i:77737 original size:14 final size:14
Alignment explanation
Indices: 77714--77746 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
77704 TATTTTAACA
77714 TTTAAAATTTT-AT
1 TTTAAAATTTTCAT
77727 TTTAGAAATTTTCAT
1 TTTA-AAATTTTCAT
77742 TTTAA
1 TTTAA
77747 TCCTCAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 8 0.44
15 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAAAATTTTCAT
Found at i:77927 original size:9 final size:9
Alignment explanation
Indices: 77913--77941 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
77903 TCATTTAATA
77913 TTTTATGAT
1 TTTTATGAT
77922 TTTTATGAT
1 TTTTATGAT
77931 TTTTATGAT
1 TTTTATGAT
77940 TT
1 TT
77942 ATATCCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TTTTATGAT
Found at i:78048 original size:19 final size:18
Alignment explanation
Indices: 78013--78051 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
78003 TGTCTTTTTA
*
78013 GTTTTCTTTCTTTTTCTT
1 GTTTTCTTTCTTATTCTT
*
78031 GTTTTTTTTCATTATTCTT
1 GTTTTCTTTC-TTATTCTT
78050 GT
1 GT
78052 AACTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.74
Consensus pattern (18 bp):
GTTTTCTTTCTTATTCTT
Found at i:85939 original size:45 final size:46
Alignment explanation
Indices: 85890--85977 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
85880 GAACATCAAA
* *
85890 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
85935 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
85978 AAGGTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Done.