Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001562.1 Hibiscus syriacus cultivar Beakdansim tig00003091_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: 68365
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2338 original size:13 final size:13
Alignment explanation
Indices: 2320--2344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2310 ATGAGAATAA
2320 ATAAAAGAAAATG
1 ATAAAAGAAAATG
2333 ATAAAAGAAAAT
1 ATAAAAGAAAAT
2345 TTGTCAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
ATAAAAGAAAATG
Found at i:6567 original size:24 final size:26
Alignment explanation
Indices: 6540--6593 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
6530 ATTCTTTTGT
6540 AAAAACAATTA-AA-TATTATTTTAA
1 AAAAACAATTACAACTATTATTTTAA
* *
6564 AAAAACAATTACAACTTTTATTTTCA
1 AAAAACAATTACAACTATTATTTTAA
6590 AAAA
1 AAAA
6594 TTGACGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.42
25 2 0.08
26 13 0.50
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAACAATTACAACTATTATTTTAA
Found at i:8555 original size:21 final size:21
Alignment explanation
Indices: 8502--8555 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
8492 TAGGCAGTAA
8502 TAGTCGGCGACATCATCAAAAC
1 TAGT-GGCGACATCATCAAAAC
* *
8524 TAGCGGTGACATCATCAAAAC
1 TAGTGGCGACATCATCAAAAC
8545 TAGTGGCGACA
1 TAGTGGCGACA
8556 ATAACTACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (21 bp):
TAGTGGCGACATCATCAAAAC
Found at i:8806 original size:15 final size:15
Alignment explanation
Indices: 8788--8829 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
8778 ATTATTGATG
*
8788 ATAATAATATTAAAA
1 ATAATAATAATAAAA
* *
8803 ATAATAACAATAACA
1 ATAATAATAATAAAA
8818 ATAATAATAATA
1 ATAATAATAATA
8830 TTTTTAAGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAA
Found at i:9237 original size:133 final size:130
Alignment explanation
Indices: 9018--9371 Score: 399
Period size: 130 Copynumber: 2.7 Consensus size: 130
9008 TCTAGTCATT
* * * * *
9018 TAAGGGTGAGACGACTCCTACATGATAAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGA
1 TAAGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCAGTGGATGACACGGTTCCTACGTGA
* * * * *
9083 TGAGGATGACTGGCCATCTTTAGGGATGATGATAACAGGGTTCCTACGCGATGAGGAC-AGTTGG
66 TGAGGATGGCT-GCCATCTTTAGGGATGATAAT-AC--GATTCCTAAGCGATGAGGACGA-CTGG
9147 TTATC
126 TTATC
* * * * *
9152 TAAGGGTGATACGACTCCTATGTGATGAGGAGGTTTAGTCAGT-GATGACATGGTTCTTACGTGA
1 TAAGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCAGTGGATGACACGGTTCCTACGTGA
* * *
9216 TGAGGATGGCATGCCATCTTTATGGATGATAATGCGATTCCTAAGTGATGAGGACGACTGGTTAT
66 TGAGGATGGC-TGCCATCTTTAGGGATGATAATACGATTCCTAAGCGATGAGGACGACTGGTTAT
9281 C
130 C
* * * * *
9282 TAAGGGTGACACTG-CTCCTACGTGATGAGGAGGCTTGGTCGGTGGATGACGCGGTTCCTATGCG
1 TAAGGGTGACAC-GACTCCTACGTGATGAGGAGGTTTGGTCAGTGGATGACACGGTTCCTACGTG
*
9346 ATGAGGACGGCTGTCCATCTTTAGGG
65 ATGAGGATGGCTG-CCATCTTTAGGG
9372 TTTTGTTTTC
Statistics
Matches: 186, Mismatches: 29, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
130 63 0.34
131 38 0.20
132 1 0.01
133 47 0.25
134 37 0.20
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (130 bp):
TAAGGGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCAGTGGATGACACGGTTCCTACGTGA
TGAGGATGGCTGCCATCTTTAGGGATGATAATACGATTCCTAAGCGATGAGGACGACTGGTTATC
Found at i:9500 original size:37 final size:37
Alignment explanation
Indices: 9440--9512 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
9430 TCAAATATGA
* *
9440 TGTTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTT
1 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATTT
9477 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATT
9513 CATTTCAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:9534 original size:36 final size:35
Alignment explanation
Indices: 9442--9535 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 35
9432 AAATATGATG
* *
9442 TTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTA
9477 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATTCA
1 T-TT-CAAGAGAAACTGTCTCAAGAGAGACAAAATT-A
*
9515 TTTCAAGGGAAAC-GATCTCAA
1 TTTCAAGAGAAACTG-TCTCAA
9536 TGTTTGTGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.04
36 17 0.33
37 32 0.62
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (35 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:10054 original size:37 final size:36
Alignment explanation
Indices: 9916--10057 Score: 146
Period size: 37 Copynumber: 3.9 Consensus size: 36
9906 CATCTCAAAG
* * *
9916 GAAAAA-TGTCTCAAGCGAGATGAAAA-TTG-TTTCA
1 GAAAAATTGTCTCAAGCAAGA-CAAAATTTGTTTTTA
* * *
9950 GAAAAATTGTCTCCAGCAAGAAAAAAATTTATTTTTA
1 GAAAAATTGTCTCAAGCAAG-ACAAAATTTGTTTTTA
* * *
9987 GAGAAAACTCTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAAATTGTCTCAAGCAAGACAAAATTTGTTTTT-A
10025 GAAAAATTGTCTCAAGCAAGACAAAATTTGTTT
1 GAAAAATTGTCTCAAGCAAGACAAAATTTGTTT
10058 CATGATGCTG
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
34 6 0.07
35 15 0.17
36 3 0.03
37 47 0.53
38 17 0.19
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (36 bp):
GAAAAATTGTCTCAAGCAAGACAAAATTTGTTTTTA
Found at i:18842 original size:14 final size:14
Alignment explanation
Indices: 18823--18852 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18813 TGGTGTGCTA
18823 GAGATATGGCATAT
1 GAGATATGGCATAT
18837 GAGATATGGCATAT
1 GAGATATGGCATAT
18851 GA
1 GA
18853 ATGATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.27
Consensus pattern (14 bp):
GAGATATGGCATAT
Found at i:23186 original size:3 final size:3
Alignment explanation
Indices: 23178--23253 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
23168 GGGTCTTGTA
*
23178 AAT AAT AAT AAT -AT AGT AAT AAT AAT AAT -AT AAT ATAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT
* *
23223 TAT ATAT AAT AAT AGT AAT AAT -AT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
23254 TCAACTCAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 46 0.74
4 10 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:23199 original size:14 final size:15
Alignment explanation
Indices: 23180--23250 Score: 73
Period size: 14 Copynumber: 4.9 Consensus size: 15
23170 GTCTTGTAAA
23180 TAATAATAAT-ATAG
1 TAATAATAATAATAG
23194 TAATAATAATAATA-
1 TAATAATAATAATAG
23208 TAATATATATATAAT--
1 TAATA-ATA-ATAATAG
23223 T-ATATATAATAATAG
1 TAATA-ATAATAATAG
23238 TAATAAT-ATAATA
1 TAATAATAATAATA
23251 ATATCAACTC
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.10
14 28 0.55
15 10 0.20
16 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:23200 original size:17 final size:16
Alignment explanation
Indices: 23178--23253 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 16
23168 GGGTCTTGTA
23178 AATAATAATAATATAGT
1 AATAATAATAATATA-T
23195 AATAATAATAATATAAT
1 AATAATAATAATAT-AT
*
23212 ATATATATAATTATATAT
1 A-ATA-ATAATAATATAT
*
23230 AATAATAGTAATAATAT
1 AATAATAATAAT-ATAT
23247 AATAATA
1 AATAATA
23254 TCAACTCAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
16 6 0.12
17 30 0.58
18 7 0.13
19 9 0.17
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATAATAATAATATAT
Found at i:23228 original size:10 final size:11
Alignment explanation
Indices: 23185--23247 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
23175 GTAAATAATA
23185 ATAATATAGTA-
1 ATAATATA-TAT
23196 ATAATA-ATAAT
1 ATAATATAT-AT
23207 ATAATATATAT
1 ATAATATATAT
23218 ATAAT-TATAT
1 ATAATATATAT
23228 ATAATA-ATAGT
1 ATAATATATA-T
23239 AATAATATA
1 -ATAATATA
23248 ATAATATCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.02
10 15 0.33
11 20 0.44
12 8 0.18
13 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
ATAATATATAT
Found at i:23510 original size:20 final size:20
Alignment explanation
Indices: 23402--23503 Score: 168
Period size: 20 Copynumber: 5.1 Consensus size: 20
23392 ATCCTACCAT
*
23402 GAGGTTTTACAGATGACCCG
1 GAGGTTTTACAAATGACCCG
*
23422 GAGGTTTTACATATGACCCG
1 GAGGTTTTACAAATGACCCG
*
23442 GAGGTTTTACAGATGACCCG
1 GAGGTTTTACAAATGACCCG
*
23462 GAGGTTTTACAAATGACCTG
1 GAGGTTTTACAAATGACCCG
23482 GAGGTTTTACAAATGACCCG
1 GAGGTTTTACAAATGACCCG
23502 GA
1 GA
23504 AGATTTAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (20 bp):
GAGGTTTTACAAATGACCCG
Found at i:23678 original size:119 final size:119
Alignment explanation
Indices: 23457--23971 Score: 814
Period size: 119 Copynumber: 4.3 Consensus size: 119
23447 TTTACAGATG
* * * * * *
23457 ACCCGGAGGTTTTACAAATGACCTGGAGGTTTTACAAATGACCCGGAAGATTTAATTTTCTAGAA
1 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
* * *
23522 CGTTAAATGAGAAACTATGAAAATCGCTTTCTCATTTTCATGCAAAAACATCCT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCT
* * * * *
23576 ACCCTGAGCCTTTACAAATGGCCCAGAGGTTTTACAAATCACCAGGAGGATTTAATTTTCTAGAA
1 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
* *
23641 CATTAAATGAGAAACTTTGAAAATTGTTTTCTCATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCT
*
23695 ACCCTAAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
1 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
* * *
23760 CATTTAATGAGAAACTTTGAAAATCGCTTTCTTATTTTCATTCGAAAACATCCT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCT
23814 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
1 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
*
23879 CATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCGAAAACATCCT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCT
* * *
23933 ACCCTGAGGCTTTACAGATGACCCAGAGGCTTTATAAAT
1 ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAAT
23972 TCATGGAAAA
Statistics
Matches: 363, Mismatches: 33, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 363 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (119 bp):
ACCCTGAGGCTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAA
CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCT
Found at i:23728 original size:20 final size:20
Alignment explanation
Indices: 23705--23748 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
23695 ACCCTAAGGC
* * *
23705 TTTACAGATGACCCGGAGGT
1 TTTACAAATCACCCGGAGGA
23725 TTTACAAATCACCCGGAGGA
1 TTTACAAATCACCCGGAGGA
23745 TTTA
1 TTTA
23749 ATTTTCTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (20 bp):
TTTACAAATCACCCGGAGGA
Found at i:23842 original size:20 final size:20
Alignment explanation
Indices: 23814--23867 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23804 AAAACATCCT
* * * *
23814 ACCCTGAGGCTTTACAGATG
1 ACCCGGAGGATTTACAAATC
*
23834 ACCCGGAGGTTTTACAAATC
1 ACCCGGAGGATTTACAAATC
23854 ACCCGGAGGATTTA
1 ACCCGGAGGATTTA
23868 ATTTTCTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
ACCCGGAGGATTTACAAATC
Found at i:29771 original size:46 final size:47
Alignment explanation
Indices: 29704--29796 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 47
29694 ATATATATAT
* * *
29704 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTTGGAAAAATAAA
1 CCTAACCGCATGCTTTCTAGTTCGCATGCATTTATTTAG-AAAATAAA
*
29750 CCTAACCGCATGGTTTCTAGTTCGCATGCATTTATTTAGAAAATAAA
1 CCTAACCGCATGCTTTCTAGTTCGCATGCATTTATTTAGAAAATAAA
29797 ATAATAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
46 21 0.51
47 13 0.32
48 7 0.17
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (47 bp):
CCTAACCGCATGCTTTCTAGTTCGCATGCATTTATTTAGAAAATAAA
Found at i:32208 original size:3 final size:3
Alignment explanation
Indices: 32200--32256 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
32190 GTTTCTTGTA
* *
32200 AAT AAT AAT -AT AAT -AT ATAT AAT TAT ATAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT
32245 AAT -AT AAT AAT A
1 AAT AAT AAT AAT A
32257 TAAACTCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.13
3 33 0.73
4 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:32214 original size:8 final size:8
Alignment explanation
Indices: 32201--32259 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
32191 TTTCTTGTAA
32201 ATAATAAT
1 ATAATAAT
32209 ATAATATAT
1 ATAATA-AT
*
32218 ATAATTAT
1 ATAATAAT
32226 AT-AT-A-
1 ATAATAAT
*
32231 ATAATAGT
1 ATAATAAT
32239 AATAATAAT
1 -ATAATAAT
32248 ATAATAAT
1 ATAATAAT
32256 ATAA
1 ATAA
32260 ACTCAGAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
5 2 0.05
6 3 0.07
7 2 0.05
8 22 0.51
9 14 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATAATAAT
Found at i:32236 original size:30 final size:30
Alignment explanation
Indices: 32200--32258 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
32190 GTTTCTTGTA
*
32200 AATAATAAT-ATAATATATATAATTATATAT
1 AATAATAATAATAATA-ATATAATAATATAT
*
32230 AATAATAGTAATAATAATATAATAATATA
1 AATAATAATAATAATAATATAATAATATA
32259 AACTCAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AATAATAATAATAATAATATAATAATATAT
Found at i:33644 original size:18 final size:18
Alignment explanation
Indices: 33623--33665 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
33613 TAATTATTTA
33623 TTTATTTTA-TCTTTATAT
1 TTTATTTTATTC-TTATAT
*
33641 TTTATTTTATTCTTATTT
1 TTTATTTTATTCTTATAT
33659 TTTATTT
1 TTTATTT
33666 CAAAACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTCTTATAT
Found at i:37979 original size:21 final size:21
Alignment explanation
Indices: 37955--38004 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
37945 AGTAATTTCA
37955 CAAGAAAAGATGGTTACATCC
1 CAAGAAAAGATGGTTACATCC
* *
37976 CAAGAAAAGCTGGTTGCATCC
1 CAAGAAAAGATGGTTACATCC
*
37997 CAGGAAAA
1 CAAGAAAA
38005 TTCCAAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAAAAGATGGTTACATCC
Found at i:39303 original size:2 final size:2
Alignment explanation
Indices: 39291--39337 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
39281 TGAAAAGAAA
39291 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39334 AT AT
1 AT AT
39338 CCTAACCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41800 original size:3 final size:3
Alignment explanation
Indices: 41792--41869 Score: 81
Period size: 3 Copynumber: 26.3 Consensus size: 3
41782 GAGTATTGTA
* *
41792 AAT AAT AAT AAT AAC AAT AAT -AT AGT AAT AAT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
41837 ATAT AAT TAT ATAT AAT AAT AGT AAT AAT AAT A
1 A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A
41870 TAGTAATATC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
2 6 0.10
3 50 0.81
4 6 0.10
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:41822 original size:17 final size:16
Alignment explanation
Indices: 41792--41869 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 16
41782 GAGTATTGTA
41792 AATAATA-ATAATAAC
1 AATAATATATAATAAC
*
41807 AATAATATAGTAATAAT
1 AATAATATA-TAATAAC
*
41824 AATAATATA-ATATATAT
1 AATAATATATA-ATA-AC
* *
41841 AATTATATATAATAAT
1 AATAATATATAATAAC
*
41857 AGTAATA-ATAATA
1 AATAATATATAATA
41870 TAGTAATATC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.26
16 11 0.20
17 28 0.52
18 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAATATATAATAAC
Found at i:42713 original size:21 final size:21
Alignment explanation
Indices: 42689--42728 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42679 TTTCCTCTGG
42689 TTTTATAAAAG-TTTTCTTTTC
1 TTTT-TAAAAGTTTTTCTTTTC
*
42710 TTTTTCAAAGTTTTTCTTT
1 TTTTTAAAAGTTTTTCTTT
42729 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTAAAAGTTTTTCTTTTC
Found at i:42733 original size:20 final size:20
Alignment explanation
Indices: 42696--42733 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42686 TGGTTTTATA
*
42696 AAAGTTTTCTTTTCTTTTTC
1 AAAGTTTTCTTTTATTTTTC
42716 AAAGTTTT-TCTTTATTTT
1 AAAGTTTTCT-TTTATTTT
42734 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (20 bp):
AAAGTTTTCTTTTATTTTTC
Found at i:43385 original size:18 final size:18
Alignment explanation
Indices: 43364--43406 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43354 TAATTAATTA
43364 TTTATTTTA-TCTTTATAT
1 TTTATTTTATTC-TTATAT
*
43382 TTTATTTTATTCTTATTT
1 TTTATTTTATTCTTATAT
43400 TTTATTT
1 TTTATTT
43407 CAAAACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTCTTATAT
Found at i:44241 original size:13 final size:13
Alignment explanation
Indices: 44219--44249 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
44209 TTTTTTGCTC
44219 AAAA-AGAAAAGA
1 AAAATAGAAAAGA
44231 AAAATAGAAAAGA
1 AAAATAGAAAAGA
44244 AAAATA
1 AAAATA
44250 TCAGCAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAATAGAAAAGA
Found at i:47726 original size:21 final size:21
Alignment explanation
Indices: 47702--47748 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
47692 AATTTCACAA
* *
47702 GAAAAGTTTGTTACATCCCAG
1 GAAAAGCTGGTTACATCCCAG
* *
47723 GAAAAGCTGGTTATATCTCAG
1 GAAAAGCTGGTTACATCCCAG
47744 GAAAA
1 GAAAA
47749 TTCCAAAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (21 bp):
GAAAAGCTGGTTACATCCCAG
Found at i:48872 original size:25 final size:25
Alignment explanation
Indices: 48834--48889 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
48824 ATTCTAATTT
48834 ATTTT-TACCTTTCTCTAAACTAAA
1 ATTTTATACCTTTCTCTAAACTAAA
48858 ATTTTATACCTTTCTCTAAACTAAA
1 ATTTTATACCTTTCTCTAAACTAAA
48883 ATTTTAT
1 ATTTTAT
48890 CTTCTGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTTATACCTTTCTCTAAACTAAA
Found at i:51895 original size:15 final size:15
Alignment explanation
Indices: 51875--51903 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51865 TTTAACATAC
51875 TTTATTTCATTTTAA
1 TTTATTTCATTTTAA
51890 TTTATTTCATTTTA
1 TTTATTTCATTTTA
51904 TTCCATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTCATTTTAA
Found at i:51917 original size:5 final size:5
Alignment explanation
Indices: 51875--51944 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
51865 TTTAACATAC
* * * ** **
51875 TTTAT TTCAT TTTAA TTTAT TTCAT TTTAT TCCAT TTTAT TTTAT TAGAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
51925 GCTTGAT TTTAT TTTAT TTT
1 --TTTAT TTTAT TTTAT TTT
51945 TCTCCGAACA
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
5 45 0.92
7 4 0.08
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.67
Consensus pattern (5 bp):
TTTAT
Found at i:55105 original size:17 final size:16
Alignment explanation
Indices: 55083--55114 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55073 CAAACACCAA
55083 TTATTATTTTATTCTAT
1 TTATTATTTT-TTCTAT
55100 TTATTATTTTTTCTA
1 TTATTATTTTTTCTA
55115 GTTTGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTATTTTTTCTAT
Found at i:55920 original size:20 final size:20
Alignment explanation
Indices: 55895--55932 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55885 TGTGTACCCG
55895 ATTAATATT-TATTTTATTTT
1 ATTAAT-TTATATTTTATTTT
55915 ATTAATTTATATTTTATT
1 ATTAATTTATATTTTATT
55933 GTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTAATTTATATTTTATTTT
Found at i:55938 original size:15 final size:15
Alignment explanation
Indices: 55900--55932 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55890 ACCCGATTAA
*
55900 TATTTATTT-TATTT
1 TATTAATTTATATTT
55914 TATTAATTTATATTT
1 TATTAATTTATATTT
55929 TATT
1 TATT
55933 GTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTAATTTATATTT
Found at i:56044 original size:21 final size:22
Alignment explanation
Indices: 56018--56090 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 22
56008 TTATAAATTT
* *
56018 AAATTATATAAT-CTAAAAATA
1 AAATTATAAAATACAAAAAATA
56039 AAATTATAAAATACAAAAAATAAAA
1 AAATTATAAAATACAAAAAAT---A
56064 TAAATTATAAAATACAAAAAATA
1 -AAATTATAAAATACAAAAAATA
56087 AAAT
1 AAAT
56091 AAAATTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 11 0.24
22 11 0.24
23 1 0.02
25 1 0.02
26 21 0.47
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATTATAAAATACAAAAAATA
Found at i:56063 original size:27 final size:27
Alignment explanation
Indices: 56033--56103 Score: 135
Period size: 26 Copynumber: 2.7 Consensus size: 27
56023 ATATAATCTA
56033 AAAATAAAATTATAAAATACAAAAAAT
1 AAAATAAAATTATAAAATACAAAAAAT
56060 AAAAT-AAATTATAAAATACAAAAAAT
1 AAAATAAAATTATAAAATACAAAAAAT
56086 AAAATAAAATTATAAAAT
1 AAAATAAAATTATAAAAT
56104 TAGAATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 26 0.60
27 17 0.40
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAATAAAATTATAAAATACAAAAAAT
Found at i:56065 original size:5 final size:5
Alignment explanation
Indices: 56044--56095 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
56034 AAATAAAATT
* *
56044 ATAAA ATACA A-AAA ATAAA ATAAA TTATAAA ATACA A-AAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA --ATAAA ATAAA ATAAA ATAAA ATAAA
56094 AT
1 AT
56096 TATAAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
7 5 0.13
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:56110 original size:14 final size:13
Alignment explanation
Indices: 56033--56103 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 13
56023 ATATAATCTA
56033 AAAATAAAATTAT
1 AAAATAAAATTAT
**
56046 AAAATACAAAAAAT
1 AAAATA-AAATTAT
56060 AAAAT-AAATTAT
1 AAAATAAAATTAT
**
56072 AAAATACAAAAAAT
1 AAAATA-AAATTAT
56086 AAAATAAAATTAT
1 AAAATAAAATTAT
56099 AAAAT
1 AAAAT
56104 TAGAATTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.21
13 16 0.34
14 21 0.45
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATTAT
Found at i:58168 original size:18 final size:17
Alignment explanation
Indices: 58138--58171 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
58128 ATATTTATTT
*
58138 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
58155 ATATCAAAAAATAATAT
1 ATAT-AAAAAATAATAT
58172 TATTGTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:59035 original size:213 final size:213
Alignment explanation
Indices: 58626--59041 Score: 647
Period size: 213 Copynumber: 2.0 Consensus size: 213
58616 ACCCTTAATG
* * *
58626 ATAATAATTGATAAGAAAATCCTAAGAGTGTAAAAAAAAGGTATTAAAACACTGATAATTAAGTT
1 ATAATAAGTGATAACAAAATCCTAAGAGTGTAAAAAAAAGGTATTAAAACACTGATAATTAAGGT
* * * *
58691 AATACTATTTTAGTAAGCTTTAATAAGTCTTATATACTTGTGAGTGTGTCAAATTACTAAAATGT
66 AATACTATTTTACTAAGCTTTAATAAGTCTGATATACTTGTAAGTGTGTCAAAGTACTAAAATGT
** * *
58756 CCTTAGAGAGGTTGAAATTACTGAATTGTCCTTATGTGCATAAGTGAATGGAATAATCTATGTTG
131 CCTTAGAGAGGTTGAAATTACAAAATTATCCTTATGTGCATAAGTAAATGGAATAATCTATGTTG
58821 ATAAAAATGCACTTAGTC
196 ATAAAAATGCACTTAGTC
58839 ATAATAAGTGATAACAAAAGT-CTAAGAGTGTAAAAAAAAGGTATTAAAACACTGATAATTAAGG
1 ATAATAAGTGATAACAAAA-TCCTAAGAGTGTAAAAAAAAGGTATTAAAACACTGATAATTAAGG
* * *
58903 TAATACTATTTTACTAAGCTTTAATAAGTCTGATATACTTGTAAGTGTGTTAGAGTACTAAGATG
65 TAATACTATTTTACTAAGCTTTAATAAGTCTGATATACTTGTAAGTGTGTCAAAGTACTAAAATG
* * *
58968 TCCTTAGAG-TGTTGAAATTACAAAATTATTCTTATGTGCATAAGTAAATGGAATTAATCTGTGT
130 TCCTTAGAGAGGTTGAAATTACAAAATTATCCTTATGTGCATAAGTAAATGGAA-TAATCTATGT
59032 TGATAAAAAT
194 TGATAAAAAT
59042 AATAAGTTTT
Statistics
Matches: 184, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
212 38 0.21
213 145 0.79
214 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (213 bp):
ATAATAAGTGATAACAAAATCCTAAGAGTGTAAAAAAAAGGTATTAAAACACTGATAATTAAGGT
AATACTATTTTACTAAGCTTTAATAAGTCTGATATACTTGTAAGTGTGTCAAAGTACTAAAATGT
CCTTAGAGAGGTTGAAATTACAAAATTATCCTTATGTGCATAAGTAAATGGAATAATCTATGTTG
ATAAAAATGCACTTAGTC
Found at i:59493 original size:30 final size:30
Alignment explanation
Indices: 59453--59517 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
59443 GGTGCTTGAG
* * *
59453 AAGCTGGGAAGGCATATGGTAGCTCATGGA
1 AAGCTAGGAAGGCATATGGCAACTCATGGA
59483 AAGCTAGGAAGGCATATGGCAACTCATGGA
1 AAGCTAGGAAGGCATATGGCAACTCATGGA
*
59513 TAGCT
1 AAGCT
59518 CACTCTCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (30 bp):
AAGCTAGGAAGGCATATGGCAACTCATGGA
Found at i:61587 original size:30 final size:29
Alignment explanation
Indices: 61537--61612 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
61527 TTGGGATGGA
* * *
61537 AGCTTATGGAAAGCTCACTATTTCTTTGGT
1 AGCTCATGG-AAGCTCACTATCTCTTTGGC
*
61567 AGCTCATGGATAGCTTACTATCTCTTTGGC
1 AGCTCATGGA-AGCTCACTATCTCTTTGGC
61597 AGCTCATGGAAGCTCA
1 AGCTCATGGAAGCTCA
61613 AGGACATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
AGCTCATGGAAGCTCACTATCTCTTTGGC
Found at i:62620 original size:23 final size:24
Alignment explanation
Indices: 62578--62623 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
62568 ACCTTCCGCT
*
62578 CATCACTCTAAATCATCCCACCTA
1 CATCACTCTAAATCAACCCACCTA
*
62602 CATCAC-CTACATCAACCCACCT
1 CATCACTCTAAATCAACCCACCT
62624 TAAACCATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.22
Consensus pattern (24 bp):
CATCACTCTAAATCAACCCACCTA
Found at i:64570 original size:4 final size:4
Alignment explanation
Indices: 64561--64594 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
64551 AAAAATATAG
* *
64561 AAAT AAAT AAAT AAGT AGAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
64595 GAAGAAAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:66019 original size:76 final size:71
Alignment explanation
Indices: 65854--66021 Score: 171
Period size: 76 Copynumber: 2.3 Consensus size: 71
65844 AAAAAAGAAC
* * *
65854 ATTTTAAAAACAATATATTATATATATGTTTTAAAAAAATTAAAATAATATAATATACATTTTCA
1 ATTTTAAAAACTATATATTATATACATCTTTTAAAAAAATTAAAATAATATAATATACATTTTCA
65919 AATAAT
66 AATAAT
* * * * *
65925 ATTTT-AAAATTATATATTATATACATACTTTCTAAAAAATGTTTTCAAAATAATGTACTATATA
1 ATTTTAAAAACTATATATTATATACAT-CTTT-TAAAAAA---ATT-AAAATAATATAATATACA
65989 GTTTTC-AA-AAT
60 -TTTTCAAATAAT
*
66000 GTTTTAAAAACTATATATTATA
1 ATTTTAAAAACTATATATTATA
66022 AATATTTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
70 18 0.23
71 8 0.10
72 7 0.09
75 9 0.11
76 32 0.41
77 5 0.06
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (71 bp):
ATTTTAAAAACTATATATTATATACATCTTTTAAAAAAATTAAAATAATATAATATACATTTTCA
AATAAT
Found at i:66113 original size:34 final size:34
Alignment explanation
Indices: 66052--66139 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
66042 TTAAAAGCCA
* *
66052 TATATTATATACATTTTTAAAATGTTTTCGAAAAC
1 TATATTATATATA-TTTCAAAATGTTTTCGAAAAC
**
66087 TATATTATATATATTTCAAAATGTTTTTTAAAAC
1 TATATTATATATATTTCAAAATGTTTTCGAAAAC
*
66121 TATA-TATATGT-TTTCAAAA
1 TATATTATATATATTTCAAAA
66140 ATACTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 8 0.17
33 6 0.12
34 22 0.46
35 12 0.25
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (34 bp):
TATATTATATATATTTCAAAATGTTTTCGAAAAC
Found at i:66884 original size:84 final size:83
Alignment explanation
Indices: 66796--67329 Score: 517
Period size: 84 Copynumber: 6.4 Consensus size: 83
66786 CCGAGTGTAA
* * *
66796 TCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTT-GGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
66861 GCCTTGGAGTTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * *
66880 TCGAACTCGAAGGTCTTTCGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC-TT-GGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*** * *
66944 TGCCCTCAAAGCTGAGTGTAA
64 TG-CCTTGGAGCTGAGCGTAG
* * * *
66965 TCGAACTCGAGGGTC-T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATGCG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
67027 CCTTGGAGTTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * * * *
67045 TCAAACTCAAAGGTCTTTGGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
67110 GCCTTGGAGTTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
67129 TTGAACTCGAAGGTCTTTGG-TGACAGATAACACTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
** *
67193 GCCCTTATAGCTGAGCATAG
65 G-CCTTGGAGCTGAGCGTAG
* * * * * *
67213 TCAAACTCGAGGGTC-T--TTGGCAGATAGCCCTTCTCGACTAAAGTTATGCTGTAAATTATGCG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
67275 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * *
67293 TCGAATTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCT
67330 AGCCATGAGT
Statistics
Matches: 361, Mismatches: 77, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
80 51 0.14
81 73 0.20
82 2 0.01
83 54 0.15
84 150 0.42
85 31 0.09
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:67009 original size:165 final size:167
Alignment explanation
Indices: 66730--67082 Score: 464
Period size: 165 Copynumber: 2.1 Consensus size: 167
66720 GACAATTTTA
* * * * * **
66730 TTGACAGATAGCCCTTCTTGCCTTGAGTTATTCTGTAACTTTGGTTTGCCTCTGAGCCGAGTGTA
1 TTGACAGATAACCCTTCTAGCCTTGAGTTATTCTGTAAC-ATGATGTGCCTCAAAGCCGAGTGTA
*
66795 ATCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTACAAATGATG
65 ATCGAACTCGAAGGTCTT--GTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACAAATGATG
* * *
66860 TGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGG
128 CGCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTT-GG
*
66901 -TGACAGATAACCCTTCTAGCCTTGAGTTATGT-TGTAA-ATGATGTGCCCTCAAAGCTGAGTGT
1 TTGACAGATAACCCTTCTAGCCTTGAGTTAT-TCTGTAACATGATGTG-CCTCAAAGCCGAGTGT
* * *
66963 AATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATGC
64 AATCGAACTCGAAGGTCTTGTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACAAATGATGC
67026 GCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTGG
129 GCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTGG
**
67065 TTGGTAGATAACCCTTCT
1 TTGACAGATAACCCTTCT
67083 CGATTTAAGT
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
164 2 0.01
165 91 0.56
168 6 0.04
169 29 0.18
170 33 0.20
171 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (167 bp):
TTGACAGATAACCCTTCTAGCCTTGAGTTATTCTGTAACATGATGTGCCTCAAAGCCGAGTGTAA
TCGAACTCGAAGGTCTTGTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACAAATGATGCGC
CTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTGG
Found at i:67096 original size:165 final size:167
Alignment explanation
Indices: 66788--67321 Score: 469
Period size: 165 Copynumber: 3.2 Consensus size: 167
66778 CCTCTGAGCC
*
66788 GAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTACA
1 GAGTGTAATCGAACTCGAAGGTCTT--GTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACA
* * *
66853 AATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTGACAGATAACCCTTCT
64 AATGATGCGCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTCGGTGACAGATAACCCTTCT
* * * * *
66918 AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGCT
129 AGACTTAAGTTATGCTGCAAATGATATGCCCTCAAAGCT
* * *
66957 GAGTGTAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAA
1 GAGTGTAATCGAACTCGAAGGTCTTGTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACAAA
** *
67020 TGATGCGCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTT-GGTTGGTAGATAACCCTTCTC
66 TGATGCGCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTCGG-TGACAGATAACCCTTCTA
* *** *
67084 GATTTAAGTTATGCTGCAAATGATATG-CCTTGGAGTT
130 GACTTAAGTTATGCTGCAAATGATATGCCCTCAAAGCT
* * * * * * * * * * * **
67121 GAGCGTAGTTGAACTCGAAGGTCTTTGGTGACAGATA-ACACTTCTAGCCTTGAGTTATGCTGTA
1 GAGTGTAATCGAACTCGAAGGTC-TTGTTGGCAGATAGCCA-TTCTCGACTTAAGCTATGATACA
* ** * * * * *
67185 AATGATGTGCCCTTATAGCTGAGCATAGTCAAACTCGAGGGTCTTT--G-G-CAGATAGCCCTTC
64 AATGATGCG-CCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTCGGTGACAGATAACCCTTC
* * * ***
67246 TCGACTAAAGTTATGCTGTAAAT--TATGCGCCTTGGAGCT
128 TAGACTTAAGTTATGCTGCAAATGATATGC-CCTCAAAGCT
* * *
67285 GAGCGTAGTCGAATTCGAAGGTCTTTGTTGGCAGATA
1 GAGTGTAATCGAACTCGAAGGTC-TTGTTGGCAGATA
67322 ACCCTTCTAG
Statistics
Matches: 306, Mismatches: 51, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
162 4 0.01
164 100 0.33
165 113 0.37
166 2 0.01
167 34 0.11
168 31 0.10
169 22 0.07
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (167 bp):
GAGTGTAATCGAACTCGAAGGTCTTGTTGGCAGATAGCCATTCTCGACTTAAGCTATGATACAAA
TGATGCGCCTTGGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTCGGTGACAGATAACCCTTCTAG
ACTTAAGTTATGCTGCAAATGATATGCCCTCAAAGCT
Found at i:67244 original size:248 final size:249
Alignment explanation
Indices: 66799--67329 Score: 814
Period size: 248 Copynumber: 2.1 Consensus size: 249
66789 AGTGTAATCG
* * * *
66799 AACTCGAAGGTCTTCGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTACAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATATGCC
*
66864 TTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTGACAGATAACCCTTCTAGCCTTGAGTT
66 TTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTGACAGATAACACTTCTAGCCTTGAGTT
* ** *
66929 ATGTTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCC
131 ATGCTGTAAATGATGTGCCCTCAAAGCTGAGCATAATCAAACTCGAGGGTCTTTGGCAGATAGCC
* *
66994 CTTCTCGACTTAAGCTATGATGCAAATGATGCGCCTTGGAGTTGAGCGTAGTCA
196 CTTCTCGACTAAAGCTATGATGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCA
* * * * *
67048 AACTCAAAGGTCTTTGGTTGGTAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATATGCC
*
67113 TTGGAGTTGAGCGTAGTTGAACTCGAAGGTCTTT-GGTGACAGATAACACTTCTAGCCTTGAGTT
66 TTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTGACAGATAACACTTCTAGCCTTGAGTT
* * *
67177 ATGCTGTAAATGATGTGCCCTTATAGCTGAGCATAGTCAAACTCGAGGGTCTTTGGCAGATAGCC
131 ATGCTGTAAATGATGTGCCCTCAAAGCTGAGCATAATCAAACTCGAGGGTCTTTGGCAGATAGCC
* * * * *
67242 CTTCTCGACTAAAGTTATGCTGTAAATTATGCGCCTTGGAGCTGAGCGTAGTCG
196 CTTCTCGACTAAAGCTATGATGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCA
*
67296 AATTCGAAGGTCTTT-GTTGGCAGATAACCCTTCT
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
67330 AGCCATGAGT
Statistics
Matches: 254, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
247 18 0.07
248 147 0.58
249 89 0.35
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (249 bp):
AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATATGCC
TTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTGACAGATAACACTTCTAGCCTTGAGTT
ATGCTGTAAATGATGTGCCCTCAAAGCTGAGCATAATCAAACTCGAGGGTCTTTGGCAGATAGCC
CTTCTCGACTAAAGCTATGATGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCA
Done.