Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007111.1 Hibiscus syriacus cultivar Beakdansim tig00018584_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: 137806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:258 original size:46 final size:46
Alignment explanation
Indices: 183--514 Score: 392
Period size: 46 Copynumber: 7.4 Consensus size: 46
173 AATACATCCG
* * * *
183 TTCATACA-TTTAATCATGACATCCTTTCATGCCCTAATGCATCAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
* * ** *
228 TTCATGCATTTTAGTTATGGTATCCTTTCATGTGTTAATGCATCTT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
* * * *
274 TTCATGCATTTCAATTATTGCATCCTTTCATGCCTTAATACATTC-G
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCA-TCAT
* * * *
320 TTCATGTA-TTTAGTTATGTCATCCTTTCATGCCTGAATGC--C-T
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
* **
362 TTCATGCATTTTAATTATGGAAT-CTTTCATGCCTTAATGCATCCG
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
* *
407 TTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
*
453 TTCATGCATTTTAATTATGGCATCCTTTCATACCTTAATGCATCAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
499 TT-ATGCATTTTAATTA
1 TTCATGCATTTTAATTA
515 CGAATTCGGT
Statistics
Matches: 241, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
42 24 0.10
43 11 0.05
44 1 0.00
45 67 0.28
46 136 0.56
47 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (46 bp):
TTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCAT
Found at i:284 original size:91 final size:91
Alignment explanation
Indices: 144--510 Score: 394
Period size: 91 Copynumber: 4.1 Consensus size: 91
134 TTATTTATTA
* * * ** * * * *
144 ATTTTAGTTAGGGTCTCTTTTCATGTATTAATACATCCGTTCATACA-TTTAATCATGACATCCT
1 ATTTTAGTTATGGTATCCTTTCATGCCTTAATGCAT-CTTTCATGCATTTTAATTATGACATCCT
* *
208 TTCATGCCCTAATGCATCATTTCATGC
65 TTCATGCCTTAATGCATCAGTTCATGC
** *
235 ATTTTAGTTATGGTATCCTTTCATGTGTTAATGCATCTTTTCATGCATTTCAATTATTG-CATCC
1 ATTTTAGTTATGGTATCCTTTCATGCCTTAATGCATC-TTTCATGCATTTTAATTA-TGACATCC
* *
299 TTTCATGCCTTAATACATTC-GTTCATGT
64 TTTCATGCCTTAATGCA-TCAGTTCATGC
*
327 A-TTTAGTTAT-GTCATCCTTTCATGCCTGAATGC--CTTTCATGCATTTTAATTATGGA-AT-C
1 ATTTTAGTTATGGT-ATCCTTTCATGCCTTAATGCATCTTTCATGCATTTTAATTAT-GACATCC
*
386 TTTCATGCCTTAATGCATCCGTTCATGC
64 TTTCATGCCTTAATGCATCAGTTCATGC
** *
414 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCT
1 ATTTTAGTTATGGTATCCTTTCATGCCTTAATGCATC-TTTCATGCATTTTAATTATGACATCCT
* *
479 TTCATACCTTAATGCATCA-TTTATGC
65 TTCATGCCTTAATGCATCAGTTCATGC
505 ATTTTA
1 ATTTTA
511 ATTACGAATT
Statistics
Matches: 235, Mismatches: 26, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
86 2 0.01
87 26 0.11
88 48 0.20
89 1 0.00
90 5 0.02
91 97 0.41
92 52 0.22
93 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (91 bp):
ATTTTAGTTATGGTATCCTTTCATGCCTTAATGCATCTTTCATGCATTTTAATTATGACATCCTT
TCATGCCTTAATGCATCAGTTCATGC
Found at i:455 original size:20 final size:20
Alignment explanation
Indices: 385--496 Score: 71
Period size: 20 Copynumber: 5.0 Consensus size: 20
375 ATTATGGAAT
385 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
* *
405 CGTTCATGCATTTTAGTTATGACATC
1 CTTTCATGC--CTTA---ATG-CATC
431 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
* *
451 ATTTCATGCATTTTAATTATGGCATC
1 CTTTCATGC--CTT-A--AT-GCATC
*
477 CTTTCATACCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
497 ATTTATGCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
20 25 0.35
21 5 0.07
22 5 0.07
23 2 0.03
24 5 0.07
25 5 0.07
26 24 0.34
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
CTTTCATGCCTTAATGCATC
Found at i:4086 original size:24 final size:24
Alignment explanation
Indices: 4054--4138 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
4044 ACAGATCTAG
*
4054 ATCAGAAATCAGAACAAAATTCAT
1 ATCAGAAATCAGAACAAAATTCAA
*
4078 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAAAATTCAA
** *
4102 ATTGGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAAAATTCAA
* *
4126 ATAAAAAATCAGA
1 ATCAGAAATCAGA
4139 TAAAATATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAA
Found at i:8677 original size:150 final size:149
Alignment explanation
Indices: 8404--8682 Score: 334
Period size: 150 Copynumber: 1.9 Consensus size: 149
8394 GTAATCCCTT
*
8404 CAACCGAACACAACATAATATATAGGTTCCCCAGAACCATACAACCCCTGCACAACAGTAAGGCC
1 CAACCGAACACAACATAATATATAGGTTCCCCAGAACCATACAACCCCTGCACAACAGCAA-GCC
* * * *
8469 CTGAGCACAACTCGATGAGCCTGCATATAGTTCCTCCAATAATACCCCCAAATAAAACATTTTCA
65 CTGAGCACAACTCGAGGAACCTGAATATAGTTCCTCCAACAATACCCCCAAATAAAACATTTTCA
8534 AAAACCATAGTAAATTCCCC
130 AAAACCATAGTAAATTCCCC
* * * * * *
8554 CAACTGAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCCCT-CACAATAGCAA-CCC
1 CAACCGAACACAACATAATATATAGGTTCCCCAGAACCATACAACCCCTGCACAACAGCAAGCCC
** *
8617 -GAGCACAAAGC-CGAGGAACCTGTAAGTATTTTTCCTCCAACAATAAACCCCC-AATTAAACAT
66 TGAGCAC-AA-CTCGAGGAACCTG-AA-TATAGTTCCTCCAACAAT--ACCCCCAAATAAAACAT
8679 TTTC
125 TTTC
8683 CTTCAATAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
146 6 0.06
147 14 0.13
148 2 0.02
149 24 0.22
150 57 0.52
151 6 0.06
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.20
Consensus pattern (149 bp):
CAACCGAACACAACATAATATATAGGTTCCCCAGAACCATACAACCCCTGCACAACAGCAAGCCC
TGAGCACAACTCGAGGAACCTGAATATAGTTCCTCCAACAATACCCCCAAATAAAACATTTTCAA
AAACCATAGTAAATTCCCC
Found at i:8760 original size:24 final size:24
Alignment explanation
Indices: 8700--8826 Score: 133
Period size: 24 Copynumber: 5.5 Consensus size: 24
8690 AAACGGAGAT
*
8700 ATCAGAAATCA-AA-AGAATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
* *
8722 ATCA-ATAT-AGAACAAAATCCAG
1 ATCAGAAATCAGAACAAAATTCAG
8744 ATCAGAAATCAGAAC--AATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
* *
8766 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACAAAATTCAG
*
8790 ATC-GAAAATCAGAACAAAATTCAA
1 ATCAG-AAATCAGAACAAAATTCAG
*
8814 ATAAGAAATCAGA
1 ATCAGAAATCAGA
8827 TAAAACATTC
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 36 0.40
23 4 0.04
24 42 0.47
25 1 0.01
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAG
Found at i:11027 original size:10 final size:10
Alignment explanation
Indices: 11012--11072 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
11002 ATTTAATGGT
11012 CGGTCAACGC
1 CGGTCAACGC
*
11022 CGGTCAAAGTTC
1 CGGTCAACG--C
* *
11034 TGGTCAACGG
1 CGGTCAACGC
*
11044 TGGTCAACGC
1 CGGTCAACGC
*
11054 CAGTCAACGC
1 CGGTCAACGC
11064 CGGTCAACG
1 CGGTCAACG
11073 GGTCAACCGG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 33 0.80
12 8 0.20
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (10 bp):
CGGTCAACGC
Found at i:13350 original size:24 final size:24
Alignment explanation
Indices: 13319--13444 Score: 99
Period size: 24 Copynumber: 5.2 Consensus size: 24
13309 CGGAGATATC
13319 AGAAATCAAAACAGAATTCAGATT
1 AGAAATCAAAACAGAATTCAGATT
* * *
13343 AGATATCATAACAGAATCCAGATT
1 AGAAATCAAAACAGAATTCAGATT
* * * *
13367 AGAAATCAGAACAAAATTTAGATA
1 AGAAATCAAAACAGAATTCAGATT
* * * * *
13391 AAAAATCATAACATAATTCAAATC
1 AGAAATCAAAACAGAATTCAGATT
* * * * *
13415 AGAAATTAGAACATAATTCAAATC
1 AGAAATCAAAACAGAATTCAGATT
13439 AGAAAT
1 AGAAAT
13445 TAGATAAAAC
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (24 bp):
AGAAATCAAAACAGAATTCAGATT
Found at i:13399 original size:48 final size:48
Alignment explanation
Indices: 13316--13434 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 48
13306 AAACGGAGAT
* * * * * *
13316 ATCAGAAATCAAAACAGAATTCAGATTAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAGATAAAAAATCATAACAGAATCCAA
* * * *
13364 ATTAGAAATCAGAACAAAATTTAGATAAAAAATCATAACATAATTCAA
1 ATCAGAAATCAGAACAAAATTCAGATAAAAAATCATAACAGAATCCAA
* *
13412 ATCAGAAATTAGAACATAATTCA
1 ATCAGAAATCAGAACAAAATTCA
13435 AATCAGAAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGAACAAAATTCAGATAAAAAATCATAACAGAATCCAA
Found at i:40376 original size:37 final size:36
Alignment explanation
Indices: 40310--40499 Score: 242
Period size: 37 Copynumber: 5.3 Consensus size: 36
40300 ATAATGTAGC
* *
40310 TTTTGAAAATATTTTTTGAAAACAT-ATAATATATAG
1 TTTTGAAAACATTTTTT-AAAACGTAATAATATATAG
40346 TTTTGAAAACATTTTTTAAAACGTAAATAATATATAG
1 TTTTGAAAACATTTTTTAAAACGT-AATAATATATAG
* *
40383 TTTTGAAAACATTTTTCAAAACGT-ATAATATATGG
1 TTTTGAAAACATTTTTTAAAACGTAATAATATATAG
** *
40418 TTTTGAAAACGCTTTTAAAAACGTATATAATATATAG
1 TTTTGAAAACATTTTTTAAAACGTA-ATAATATATAG
* * *
40455 TTTTGAAAATATTTTTGAAAACGT-ATAATATATGG
1 TTTTGAAAACATTTTTTAAAACGTAATAATATATAG
40490 TTTTGAAAAC
1 TTTTGAAAAC
40500 GTATATAATA
Statistics
Matches: 136, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
35 56 0.41
36 16 0.12
37 64 0.47
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTTGAAAACATTTTTTAAAACGTAATAATATATAG
Found at i:40493 original size:23 final size:23
Alignment explanation
Indices: 40467--40522 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
40457 TTGAAAATAT
*
40467 TTTTGAAAACGTATA-ATATATGG
1 TTTTGAAAACGTATATA-ATATAG
40490 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAACGTATATAATATAG
*
40513 CTTTGAAAAC
1 TTTTGAAAAC
40523 ATATTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (23 bp):
TTTTGAAAACGTATATAATATAG
Found at i:40500 original size:72 final size:72
Alignment explanation
Indices: 40310--40500 Score: 301
Period size: 72 Copynumber: 2.6 Consensus size: 72
40300 ATAATGTAGC
* * ** *
40310 TTTTGAAAATATTTTTTGAAAACATATAATATATAGTTTTGAAAACATTTTTTAAAACGTAAATA
1 TTTTGAAAATA-TTTTTGAAAACGTATAATATATGGTTTTGAAAACGCTTTTAAAAACGTAAATA
40375 ATATATAG
65 ATATATAG
* * *
40383 TTTTGAAAACATTTTTCAAAACGTATAATATATGGTTTTGAAAACGCTTTTAAAAACGTATATAA
1 TTTTGAAAATATTTTTGAAAACGTATAATATATGGTTTTGAAAACGCTTTTAAAAACGTAAATAA
40448 TATATAG
66 TATATAG
40455 TTTTGAAAATATTTTTGAAAACGTATAATATATGGTTTTGAAAACG
1 TTTTGAAAATATTTTTGAAAACGTATAATATATGGTTTTGAAAACG
40501 TATATAATAT
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 98 0.91
73 10 0.09
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (72 bp):
TTTTGAAAATATTTTTGAAAACGTATAATATATGGTTTTGAAAACGCTTTTAAAAACGTAAATAA
TATATAG
Found at i:40544 original size:58 final size:60
Alignment explanation
Indices: 40430--40556 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 60
40420 TTGAAAACGC
* * **
40430 TTTTAAAAACGTATATAATATATAGTTTTGAAAATATTTTTGAAAACGTATAATATATGG
1 TTTTAAAAACGTATATAATATATAGCTTTGAAAACATTTTTGAAAAAATATAATATATGG
* *
40490 TTTTGAAAACGTATAT-A-ATATAGCTTTGAAAACATATTTTGAAAAAATAT-ATATATGT
1 TTTTAAAAACGTATATAATATATAGCTTTGAAAACAT-TTTTGAAAAAATATAATATATGG
*
40548 TTTTTAAAA
1 TTTTAAAAA
40557 TGATTTTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 31 0.53
59 13 0.22
60 15 0.25
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (60 bp):
TTTTAAAAACGTATATAATATATAGCTTTGAAAACATTTTTGAAAAAATATAATATATGG
Found at i:40663 original size:11 final size:9
Alignment explanation
Indices: 40640--40704 Score: 69
Period size: 9 Copynumber: 6.8 Consensus size: 9
40630 ATTTCATTTC
*
40640 ATTATATAT
1 ATTATTTAT
40649 ATTATATTAAT
1 ATTAT-TT-AT
40660 ATTATTTAT
1 ATTATTTAT
40669 ATTATTTAT
1 ATTATTTAT
40678 ATTTTATTTATT
1 A--TTATTTA-T
40690 ATTATTTAT
1 ATTATTTAT
40699 -TTATTT
1 ATTATTT
40705 TTTCAGGTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
8 6 0.12
9 18 0.36
10 10 0.20
11 14 0.28
12 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTATTTAT
Found at i:40679 original size:18 final size:18
Alignment explanation
Indices: 40640--40704 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 18
40630 ATTTCATTTC
*
40640 ATTATATATATTATATTAAT
1 ATTATTTATATTAT-TT-AT
40660 ATTATTTATATTATTTAT
1 ATTATTTATATTATTTAT
40678 ATTTTATTTATTATTATTTAT
1 A--TTATTTA-TATTATTTAT
40699 -TTATTT
1 ATTATTT
40705 TTTCAGGTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 9 0.22
19 2 0.05
20 20 0.49
21 10 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATTTATATTATTTAT
Found at i:54086 original size:23 final size:23
Alignment explanation
Indices: 54049--54113 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
54039 GTTTTTGAAA
*
54049 ATAGTTTTTGGAAACATATA-ATAT
1 ATAG-TTTTGAAAACATATATA-AT
*
54073 ATAGTTTTGAAAACGTATATAAT
1 ATAGTTTTGAAAACATATATAAT
*
54096 ATAGTTTTAAAAACATAT
1 ATAGTTTTGAAAACATAT
54114 TTTGAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 31 0.86
24 5 0.14
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.40
Consensus pattern (23 bp):
ATAGTTTTGAAAACATATATAAT
Found at i:54215 original size:13 final size:12
Alignment explanation
Indices: 54189--54262 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
54179 ATATACTTAC
54189 ATATTA-TATATT
1 ATATTATTAT-TT
54201 ATATTAATTATTT
1 ATATT-ATTATTT
*
54214 ATATT-TTTTATT
1 ATATTATTAT-TT
54226 ATATT-TT-TTT
1 ATATTATTATTT
*
54236 ATATTA-TAGTT
1 ATATTATTATTT
54247 ATTATTATTTATTT
1 A-TATTA-TTATTT
54261 AT
1 AT
54263 TTTTTCAGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
10 8 0.16
11 7 0.14
12 19 0.37
13 9 0.18
14 8 0.16
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (12 bp):
ATATTATTATTT
Found at i:54217 original size:25 final size:24
Alignment explanation
Indices: 54189--54262 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 24
54179 ATATACTTAC
54189 ATATTATATATTATATTAATTATTT
1 ATATTATATATTATATT-ATTATTT
* *
54214 ATATTTTTTATTATATT-TT-TTT
1 ATATTATATATTATATTATTATTT
*
54236 ATATTATA-GTTATTATTATTTATTT
1 ATATTATATATTA-TATTA-TTATTT
54261 AT
1 AT
54263 TTTTTCAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 3 0.08
22 13 0.32
23 2 0.05
24 2 0.05
25 20 0.50
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (24 bp):
ATATTATATATTATATTATTATTT
Found at i:58759 original size:24 final size:23
Alignment explanation
Indices: 58732--58821 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 23
58722 TCTTATTTGA
*
58732 ATTCTGTTATGATACCTGACTTGG
1 ATTCTGATATGATA-CTGACTTGG
58756 ATTCTGATATGATACTGA-TATGG
1 ATTCTGATATGATACTGACT-TGG
* *
58779 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATAC-TGACTTGG
*
58803 ATTCTGATCTGATACTGAC
1 ATTCTGATATGATACTGAC
58822 CTGAATTATA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
22 1 0.02
23 25 0.42
24 34 0.57
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTCTGATATGATACTGACTTGG
Found at i:59971 original size:23 final size:23
Alignment explanation
Indices: 59953--60046 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
59943 TGCCACATAA
*
59953 AAATGTCCCGAATGACCACGTAG
1 AAATGTCCCGAAGGACCACGTAG
*
59976 AAATGTCCCGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCACGTAG
*
59999 AAATGTCCCAAAGGACCACGTAG
1 AAATGTCCCGAAGGACCACGTAG
* * *
60022 AATTGTCCTGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCACGTAG
60045 AA
1 AA
60047 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (23 bp):
AAATGTCCCGAAGGACCACGTAG
Found at i:60003 original size:46 final size:46
Alignment explanation
Indices: 59953--60046 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
59943 TGCCACATAA
* *
59953 AAATGTCCCGAATGACCACGTAGAAATGTCCCGAAGGACCGCGTAG
1 AAATGTCCCAAAGGACCACGTAGAAATGTCCCGAAGGACCGCGTAG
* *
59999 AAATGTCCCAAAGGACCACGTAGAATTGTCCTGAAGGACCGCGTAG
1 AAATGTCCCAAAGGACCACGTAGAAATGTCCCGAAGGACCGCGTAG
60045 AA
1 AA
60047 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (46 bp):
AAATGTCCCAAAGGACCACGTAGAAATGTCCCGAAGGACCGCGTAG
Found at i:62402 original size:13 final size:13
Alignment explanation
Indices: 62360--62406 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
62350 TTATATCTAC
*
62360 TATTATTTTCTTTA
1 TATT-TTTTATTTA
* *
62374 TA-TTTCTATTTC
1 TATTTTTTATTTA
62386 TATTTTTTATTTA
1 TATTTTTTATTTA
62399 TATTTTTT
1 TATTTTTT
62407 TTATTTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 8 0.30
13 17 0.63
14 2 0.07
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:62977 original size:13 final size:14
Alignment explanation
Indices: 62947--62977 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
62937 AATCGAAAAG
62947 AAAAGAAAAAGGGA
1 AAAAGAAAAAGGGA
62961 AAAAGAAAAA-GGA
1 AAAAGAAAAAGGGA
62974 AAAA
1 AAAA
62978 TAGTGGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGGGA
Found at i:64681 original size:131 final size:131
Alignment explanation
Indices: 64517--64872 Score: 489
Period size: 131 Copynumber: 2.7 Consensus size: 131
64507 TTAATATTGA
* * * * *
64517 GAATAGTAATATCTTTTTATTTCGTTTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
1 GAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
* * * * * * *
64582 TTATTCTCGATTGAAAATAATTTGATATTGTTGTTTTCTCTCGAATTAATATCAATTTTTAAGAT
66 TTATTCTCGATTGAAAATAATTAGATATTCTCGATTTCACTCGAATTAATATCAAATTTTAAGAC
64647 G
131 G
* *
64648 GAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGACTGGTTTAAGGTATGAGAGGTCAT
1 GAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
* * * *
64713 TTATTCTCGATTGGAAATCATTAGATATTCTCGATTTCACTCGAATTGATATTAAATTTTAAGAC
66 TTATTCTCGATTGAAAATAATTAGATATTCTCGATTTCACTCGAATTAATATCAAATTTTAAGAC
64778 G
131 G
* * * *
64779 GAATAATGATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGATCAT
1 GAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
*
64844 TTATTCTCAATT-AGAAATAATTAGATATT
66 TTATTCTCGATTGA-AAATAATTAGATATT
64873 ATCGTTCTCT
Statistics
Matches: 197, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
131 197 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (131 bp):
GAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
TTATTCTCGATTGAAAATAATTAGATATTCTCGATTTCACTCGAATTAATATCAAATTTTAAGAC
G
Found at i:67428 original size:17 final size:19
Alignment explanation
Indices: 67385--67430 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
67375 TATGTATTCT
67385 TATTAAATTATAATATTGA
1 TATTAAATTATAATATTGA
* * *
67404 AATAAAATT-T-ATATTTA
1 TATTAAATTATAATATTGA
67421 TATTAAATTA
1 TATTAAATTA
67431 AGTCTAATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
17 13 0.62
18 1 0.05
19 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATTATAATATTGA
Found at i:72797 original size:25 final size:25
Alignment explanation
Indices: 72769--72828 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
72759 GAAAAAAATG
*
72769 AATAAATGAAAAAAT-GAA-GAATAAA
1 AATAAAT-AAAAAATAAAAGGAA-AAA
*
72794 AATAAGTAAAAAATAAAAGGAAAAA
1 AATAAATAAAAAATAAAAGGAAAAA
72819 AATAAATAAA
1 AATAAATAAA
72829 TAAAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 7 0.23
25 20 0.67
26 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (25 bp):
AATAAATAAAAAATAAAAGGAAAAA
Found at i:72817 original size:22 final size:22
Alignment explanation
Indices: 72791--72833 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
72781 AATGAAGAAT
72791 AAAAATAAGTAAA-AAATAAAAGG
1 AAAAA-AA-TAAATAAATAAAAGG
72814 AAAAAAATAAATAAATAAAA
1 AAAAAAATAAATAAATAAAA
72834 TATTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAAATAAATAAATAAAAGG
Found at i:72846 original size:2 final size:2
Alignment explanation
Indices: 72839--72881 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
72829 TAAAATATTA
*
72839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72881 A
1 A
72882 AATGAGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:72999 original size:29 final size:30
Alignment explanation
Indices: 72932--72999 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
72922 AGTAATATGA
*
72932 AAATAT-AATATAATATAAATAAAAAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
* * * *
72961 AAAAACAAAAATAA-ATAAATATATAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
72990 AAATATAAAA
1 AAATATAAAA
73000 GTATACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATATAAAAATAATATAAATAAAAAAACC
Found at i:73180 original size:19 final size:19
Alignment explanation
Indices: 73133--73186 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
73123 TTATAAGTAA
*
73133 AGTATTAAAAAAGTATATAT
1 AGTATTAAAAAA-TAAATAT
*
73153 A-TATATAAATAATAAATAT
1 AGTAT-TAAAAAATAAATAT
73172 AGTATTAAAAAATAA
1 AGTATTAAAAAATAA
73187 CCAAATGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AGTATTAAAAAATAAATAT
Found at i:73758 original size:37 final size:36
Alignment explanation
Indices: 73717--73809 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
73707 AGATCTTATC
* *
73717 TTTAGGAGTTT-AAATCATAGTAGAACTT-TATCCTATT
1 TTTAGGAGTTTGAAATC-TAGCA-AAATTCTATCCTA-T
*
73754 TTTAGGAGTTTGAATTCTAGCAAAATTCTATCCTAT
1 TTTAGGAGTTTGAAATCTAGCAAAATTCTATCCTAT
*
73790 TTTAGGAGTTTGAATTCTAG
1 TTTAGGAGTTTGAAATCTAG
73810 TAGGACGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
36 25 0.49
37 22 0.43
38 4 0.08
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTAGGAGTTTGAAATCTAGCAAAATTCTATCCTAT
Found at i:74826 original size:106 final size:106
Alignment explanation
Indices: 74508--75565 Score: 1583
Period size: 106 Copynumber: 10.0 Consensus size: 106
74498 GCATTGTTCC
* * * * *
74508 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * *
74573 CCAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
74614 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *** * ** *
74673 TCAGCCACCCCTTCGTCATGAAGTTGGGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * **
74715 G-GTCCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGGAAGCTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
74779 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
74820 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
74885 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
74926 GAGTCCAATATCCTTCGCTGCGAAGTTGAAACTGGCTCTGAAATTGGGAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
74990 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
75031 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
75096 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
75137 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
75202 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
75243 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
75308 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
75349 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
75414 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * ** *
75455 GAGTCCAAAATTCTTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGATGTTGTTTGTTGACA
1 GAGTCCAATA-TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * *
75520 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
75562 GAGT
1 GAGT
75566 GGCACGATAT
Statistics
Matches: 874, Mismatches: 68, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
100 76 0.09
101 5 0.01
102 5 0.01
104 4 0.00
105 101 0.12
106 591 0.68
107 92 0.11
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:75343 original size:423 final size:424
Alignment explanation
Indices: 74508--75565 Score: 1700
Period size: 423 Copynumber: 2.5 Consensus size: 424
74498 GCATTGTTCC
* * * *
74508 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
74573 CCAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* * ** *
74638 GTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAATCAGCCACCCCTTCGTCATGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
** *
74697 TGGGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGG
196 TGAACTTGTGTTGTC-TGGAGTCCAAGATCCTTCGATGAGAAGTTAAAATTGGCTCTGAAATTGG
*
74761 GAAGCTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
260 GAAGCTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
74826 AATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCG
325 AATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCG
74891 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
390 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
74926 GAGTCCAATATCCTTCGCTGCGAAGTTGAAACTGGCTCTGAAATTGGGAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
74990 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* *
75055 GTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
* * * *
75120 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTGTGTTGTCTGGAGTCCAAGATCCTTCGATGAGAAGTTAAAATTGGCTCTGAAATTGGG
* *
75185 AAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTTCA
261 AAGCTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
75250 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
326 ATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG
75315 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
391 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
75349 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * * *
75414 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAAATTCTTTCGCTGTGA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATA-TCCTTCGCTGTGA
* * *
75479 AATTGAAATTGGCTCTGAAATTGGGATGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAG
*
75544 TTGAACTTGTGTTGTCTCGAGT
195 TTGAACTTGTGTTGTCTGGAGT
75566 GGCACGATAT
Statistics
Matches: 588, Mismatches: 43, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
417 87 0.15
418 50 0.09
419 3 0.01
420 2 0.00
422 4 0.01
423 295 0.50
424 55 0.09
425 92 0.16
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (424 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
TGAACTTGTGTTGTCTGGAGTCCAAGATCCTTCGATGAGAAGTTAAAATTGGCTCTGAAATTGGG
AAGCTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:77177 original size:9 final size:8
Alignment explanation
Indices: 77157--77228 Score: 67
Period size: 8 Copynumber: 8.8 Consensus size: 8
77147 ATTTTTGTTA
77157 TTTCTTTT
1 TTTCTTTT
77165 TTTCTTTT
1 TTTCTTTT
77173 GTTTCTCTTT
1 -TTTCT-TTT
77183 TTTCTTTGT
1 TTTCTTT-T
77192 TTT-TTTT
1 TTTCTTTT
*
77199 CTTCTTTT
1 TTTCTTTT
77207 TCTTCTTTT
1 T-TTCTTTT
*
77216 CTT-TTTT
1 TTTCTTTT
*
77223 GTTCTT
1 TTTCTT
77229 GATTGGATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 9 0.17
8 21 0.39
9 21 0.39
10 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (8 bp):
TTTCTTTT
Found at i:77182 original size:39 final size:39
Alignment explanation
Indices: 77134--77222 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 39
77124 TTTTTTGACC
77134 CTTTT-TCTTTTTAATTT-TTGTTATTTCTT-TTTTTCTT
1 CTTTTCTCTTTTTAATTTGTT-TTATTTCTTCTTTTTCTT
* ** *
77171 TTGTTTCTCTTTTTTCTTTGTTTTTTTTCTTCTTTTTCTT
1 CT-TTTCTCTTTTTAATTTGTTTTATTTCTTCTTTTTCTT
77211 CTTTTCT-TTTTT
1 CTTTTCTCTTTTT
77223 GTTCTTGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
37 1 0.02
38 8 0.19
39 23 0.53
40 11 0.26
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (39 bp):
CTTTTCTCTTTTTAATTTGTTTTATTTCTTCTTTTTCTT
Found at i:77183 original size:17 final size:17
Alignment explanation
Indices: 77157--77225 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
77147 ATTTTTGTTA
77157 TTTCTTTTTTTCTTTTG
1 TTTCTTTTTTTCTTTTG
77174 TTTCTCTTTTTTC-TTTG
1 TTTCT-TTTTTTCTTTTG
77191 TTT-TTTTTCTTCTTTT-
1 TTTCTTTTT-TTCTTTTG
*
77207 TCTTCTTTTCTT-TTTTG
1 T-TTCTTTTTTTCTTTTG
77224 TT
1 TT
77226 CTTGATTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
15 4 0.09
16 10 0.22
17 20 0.44
18 11 0.24
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTTTCTTTTG
Found at i:77199 original size:31 final size:33
Alignment explanation
Indices: 77161--77225 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
77151 TTGTTATTTC
77161 TTTTTTTCTT-TTGTTTC-TCTTTT-TTCTTTGT
1 TTTTTTTCTTCTT-TTTCTTCTTTTCTTCTTTGT
*
77192 TTTTTTTCTTCTTTTTCTTCTTTTCTTTTTTGT
1 TTTTTTTCTTCTTTTTCTTCTTTTCTTCTTTGT
77225 T
1 T
77226 CTTGATTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 14 0.47
32 8 0.27
33 8 0.27
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (33 bp):
TTTTTTTCTTCTTTTTCTTCTTTTCTTCTTTGT
Found at i:77220 original size:22 final size:21
Alignment explanation
Indices: 77158--77220 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
77148 TTTTTGTTAT
*
77158 TTCTTTTT-TTCTTTTGTTTC
1 TTCTTTTTCTTCTTTTTTTTC
*
77178 -TCTTTTTTCTTTGTTTTTTTTC
1 TTC-TTTTTC-TTCTTTTTTTTC
77200 TTCTTTTTCTTCTTTTCTTTT
1 TTCTTTTTCTTCTTTT-TTTT
77221 TTGTTCTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 6 0.17
22 20 0.57
23 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (21 bp):
TTCTTTTTCTTCTTTTTTTTC
Found at i:86620 original size:21 final size:21
Alignment explanation
Indices: 86566--86626 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
86556 CCCCCCCCTT
***
86566 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC-CACA
86588 AGGGGAACCGATTCCCCCCACA
1 A-GGGAACCGATTCCCCCCACA
* *
86610 AGGGAATCGATACCCCC
1 AGGGAACCGATTCCCCC
86627 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 14 0.42
22 3 0.09
23 16 0.48
ACGTcount: A:0.26, C:0.36, G:0.23, T:0.15
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCACA
Found at i:88605 original size:17 final size:17
Alignment explanation
Indices: 88572--88616 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
88562 TTTCAACATT
*
88572 TTGGATGTTTTTGGATTG
1 TTGGAT-TTTGTGGATTG
*
88590 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
88607 TTGGATTTTG
1 TTGGATTTTG
88617 GATTTATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.11, C:0.00, G:0.31, T:0.58
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:89371 original size:77 final size:75
Alignment explanation
Indices: 89205--89412 Score: 269
Period size: 77 Copynumber: 2.7 Consensus size: 75
89195 CAAAGCCAAA
* * **
89205 AATTCCAGATTGCTCAGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
89269 TTTGGCCCCGAG
64 TTTGGCCCCGAG
*
89281 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAG
1 AATTCCAG-ATGCTCGGAGGGAACCGATT-CCCCCCCATAGGAGGAACCGATTCCCCCTAAACAG
* *
89346 TTTTGCTCCGAG
64 TTTGGCCCCGAG
* *
89358 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCC
89413 CTTGTACAAC
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
74 17 0.14
75 8 0.07
76 26 0.22
77 45 0.38
78 22 0.19
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (75 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCCCCGAG
Found at i:91381 original size:18 final size:18
Alignment explanation
Indices: 91358--91429 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
91348 TGTTAGAGGG
*
91358 AAAAAATGAATAAATGAA
1 AAAAAATAAATAAATGAA
91376 AAAAAA-AGAATAAAAAT-AA
1 AAAAAATA-AAT--AAATGAA
* *
91395 GTAAAAAATAAATAAAAGGA
1 --AAAAAATAAATAAATGAA
91415 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
91430 AAATAAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
18 23 0.53
19 5 0.12
20 5 0.12
21 9 0.21
22 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAAAATAAATAAATGAA
Found at i:91443 original size:39 final size:37
Alignment explanation
Indices: 91361--91443 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 37
91351 TAGAGGGAAA
*
91361 AAATG-AATAAATGAAAAAAAAAGAATAAAAATAAGT
1 AAATGAAATAAATGAAAAAAAAAGAATAAAAATAAAT
91397 AAA--AAATAAAT-AAAAGGAAAAA-AATAAATAAATAAAT
1 AAATGAAATAAATGAAAA--AAAAAGAAT-AA-AAATAAAT
91434 AAATGAAATA
1 AAATGAAATA
91444 TTAATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
34 4 0.10
35 10 0.26
36 10 0.26
37 10 0.26
39 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (37 bp):
AAATGAAATAAATGAAAAAAAAAGAATAAAAATAAAT
Found at i:91736 original size:2 final size:2
Alignment explanation
Indices: 91731--91774 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
91721 TAAAAAAACA
* *
91731 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AA AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91771 AT AT
1 AT AT
91775 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:91774 original size:55 final size:54
Alignment explanation
Indices: 91673--91781 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 54
91663 AAAGATAATT
** * *
91673 ACAATATATATATATATATAGTAATAATACGCTTATAAGTAAAATATTTAAAAAA
1 ACAATATATATATATATATAGTAATAATACAATAATAAATAAAATA-TTAAAAAA
*
91728 ACAATATATATATATATATA-TATATATATA-AATAATAAATATAATATTAAAAAA
1 ACAATATATATATATATATAGTA-ATA-ATACAATAATAAATAAAATATTAAAAAA
91782 TAACCAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
54 10 0.21
55 34 0.72
56 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (54 bp):
ACAATATATATATATATATAGTAATAATACAATAATAAATAAAATATTAAAAAA
Found at i:91778 original size:19 final size:21
Alignment explanation
Indices: 91745--91837 Score: 59
Period size: 21 Copynumber: 4.3 Consensus size: 21
91735 ATATATATAT
*
91745 ATATATATATATAAATAATAA
1 ATATATATATATAAAAAATAA
91766 ATATA-ATAT-TAAAAAATAA
1 ATATATATATATAAAAAATAA
* *
91785 CCAAATGAATATAAATAAATAAA-AA
1 --ATAT--ATATATATAAA-AAATAA
* *
91810 ATATATGTATATATAATAAT-A
1 ATATATATATATA-AAAAATAA
91831 ATATATA
1 ATATATA
91838 GTGTAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
19 9 0.16
20 4 0.07
21 24 0.44
22 2 0.04
23 4 0.07
24 3 0.05
25 6 0.11
26 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATATATATATAAAAAATAA
Found at i:92402 original size:37 final size:37
Alignment explanation
Indices: 92317--92405 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
92307 GAATCCTAAC
* * * *
92317 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCATAGAAAAACTCTATCATATT
* *
92354 TTTAGGAGTTTGAATCCTAGAAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCATAGAAAAACTCTATCATATT
92391 TTTAGGAGTTTGAAT
1 TTTAGGAGTTTGAAT
92406 TCTAATAGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAGAAAAACTCTATCATATT
Found at i:93955 original size:37 final size:38
Alignment explanation
Indices: 93884--93957 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
93874 GAACCCAATC
93884 CGACCCGAATATCACACTTATAAAAACCCGACCCGACT
1 CGACCCGAATATCACACTTATAAAAACCCGACCCGACT
* *
93922 CGACCCGAATATCATACTTA-AAAAATCCGACCCGAC
1 CGACCCGAATATCACACTTATAAAAACCCGACCCGAC
93958 CCGAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.38, C:0.35, G:0.11, T:0.16
Consensus pattern (38 bp):
CGACCCGAATATCACACTTATAAAAACCCGACCCGACT
Found at i:93989 original size:63 final size:61
Alignment explanation
Indices: 93914--94032 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 61
93904 TAAAAACCCG
* *
93914 ACCCGACTCGACCCGAATATCAT-ACTTAAAAAATCCGACCCGACCCGAACAAAATAAAGTTTC
1 ACCCGACCCGACCCGAATAT-ATAAATT-AAAAATCCGACCCGACCCGAA-AAAATAAAGTTTC
* *
93977 ACCCGACCCGACCCGAATATATAAATTAGAAATCCGACCCGACCCGAAATAATAAA
1 ACCCGACCCGACCCGAATATATAAATTAAAAATCCGACCCGACCCGAAAAAATAAA
94033 AAAATTATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 7 0.14
62 22 0.43
63 22 0.43
ACGTcount: A:0.41, C:0.31, G:0.12, T:0.16
Consensus pattern (61 bp):
ACCCGACCCGACCCGAATATATAAATTAAAAATCCGACCCGACCCGAAAAAATAAAGTTTC
Found at i:111169 original size:21 final size:20
Alignment explanation
Indices: 111104--111172 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
111094 TTTTTATAAT
111104 AATATATAGTATA-ATTT-A
1 AATATATAGTATATATTTAA
*
111122 AA-ATA-AGTATATAATAATAA
1 AATATATAGTATAT-AT-TTAA
*
111142 TATATATAGTATATAGTTTAA
1 AATATATAGTATATA-TTTAA
111163 AATATATAGT
1 AATATATAGT
111173 TTTAGAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.15
17 3 0.08
18 4 0.10
19 1 0.03
20 2 0.05
21 16 0.40
22 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
AATATATAGTATATATTTAA
Found at i:111214 original size:48 final size:48
Alignment explanation
Indices: 111134--111266 Score: 125
Period size: 48 Copynumber: 2.8 Consensus size: 48
111124 ATAAGTATAT
*
111134 AATAATA-ATATATATAGTATA-TAGTTTAAAATATATAGT-T-T-TAGAG
1 AATAATATATATATATAGTATAGT--TTTTAAATATATAGTATATGT-GAG
*
111180 AAATAATATATATATATAGTATAGTCTTTTAAATATA-AGTATATGTGTG
1 -AATAATATATATATATAGTATAGT-TTTTAAATATATAGTATATGTGAG
* * *
111229 TATATATATATATATGTAGTATAGTATTTAAATATATA
1 AATA-ATATATATATATAGTATAGTTTTTAAATATATA
111267 AATATGATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
47 10 0.14
48 38 0.52
49 24 0.33
50 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.44
Consensus pattern (48 bp):
AATAATATATATATATAGTATAGTTTTTAAATATATAGTATATGTGAG
Found at i:111346 original size:3 final size:3
Alignment explanation
Indices: 111338--111412 Score: 125
Period size: 3 Copynumber: 25.0 Consensus size: 3
111328 GTTTTATTTA
111338 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
111386 TAT TAT TAT TAT TCAT TTT TA- TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT
111413 ATGATTGAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:112260 original size:33 final size:33
Alignment explanation
Indices: 112213--112316 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
112203 ACAAAGTTTA
*
112213 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAATACTTCCAAGTT
112245 CGATAAATTCAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAATACTTCCAAGTT
*
112278 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAATACTTCCAAGTT
112311 CGATAA
1 CGATAA
112317 TTGAAACAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 4 0.06
33 65 0.94
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAATACTTCCAAGTT
Found at i:112336 original size:21 final size:21
Alignment explanation
Indices: 112311--112352 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
112301 CTTCCAAGTT
112311 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
112332 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
112353 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:114734 original size:13 final size:13
Alignment explanation
Indices: 114716--114740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
114706 TTTTTTCCCA
114716 AACCGGTTAAAAT
1 AACCGGTTAAAAT
114729 AACCGGTTAAAA
1 AACCGGTTAAAA
114741 AAATCCGATC
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:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:116406 original size:18 final size:18
Alignment explanation
Indices: 116383--116428 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
116373 TAAATGAAAC
116383 CCTAAAATTTTGTTTTCA
1 CCTAAAATTTTGTTTTCA
116401 CCTAAAATTTTGTTTTCA
1 CCTAAAATTTTGTTTTCA
116419 CCTAAAATTT
1 CCTAAAATTT
116429 AGGAATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (18 bp):
CCTAAAATTTTGTTTTCA
Done.