Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_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: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 7
Found at i:258974 original size:32 final size:33
Alignment explanation
Indices: 258927--259017 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
258917 ACAAATCGCA
*
258927 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
258960 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
258992 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
259018 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:259036 original size:20 final size:19
Alignment explanation
Indices: 259002--259056 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
258992 TTGCGATTTT
*
259002 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
259021 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
259041 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
259057 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:259582 original size:18 final size:18
Alignment explanation
Indices: 259540--259582 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
259530 CGATCAGATG
* *
259540 ATGGCTCTGGGTGAGGTG
1 ATGGCTCTGGGCGAGGTA
*
259558 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTGGGCGAGGTA
259576 ATGGCTC
1 ATGGCTC
259583 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (18 bp):
ATGGCTCTGGGCGAGGTA
Found at i:260927 original size:20 final size:20
Alignment explanation
Indices: 260902--260944 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
260892 AATAGTTTCT
260902 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
260922 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
260942 GAA
1 GAA
260945 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:260950 original size:20 final size:20
Alignment explanation
Indices: 260912--260980 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
260902 GAAAATGAAA
* **
260912 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
260932 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
260952 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
260972 ATCGCAACG
1 ATCGCAACG
260981 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:261543 original size:20 final size:20
Alignment explanation
Indices: 261450--261543 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
261440 GATTATGTAT
*
261450 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
261470 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
261490 TATCTCGTTGCGATAGTAAG
1 TATCGCGTTGCGATAGTCAG
*
261510 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
261530 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
261544 TTTCCCAATT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:261654 original size:21 final size:21
Alignment explanation
Indices: 261614--261654 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
261604 ACTGTAGACC
** *
261614 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATACAACT
261635 ATCGCAACGCGAAATACAAC
1 ATCGCAACGCGAAATACAAC
261655 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATACAACT
Found at i:262517 original size:29 final size:29
Alignment explanation
Indices: 262484--262572 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
262474 ACGATTGACT
262484 GATAATAATTATCTTATTTGAAAGCAGTA
1 GATAATAATTATCTTATTTGAAAGCAGTA
* * * *
262513 GATAAT-A-TAT-TAATAT-ACAA-CTGATT
1 GATAATAATTATCTTATTTGA-AAGCAG-TA
262539 GATAATAATTATCTTATTTGAAAGCAGTA
1 GATAATAATTATCTTATTTGAAAGCAGTA
262568 GATAA
1 GATAA
262573 CTCAAGTATG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.29
27 4 0.09
28 4 0.09
29 18 0.40
30 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (29 bp):
GATAATAATTATCTTATTTGAAAGCAGTA
Found at i:262542 original size:55 final size:54
Alignment explanation
Indices: 262457--262572 Score: 187
Period size: 55 Copynumber: 2.1 Consensus size: 54
262447 TCAGATTTTC
* * *
262457 TAGATTATATATAATATACGATTGACTGATAATAATTATCTTATTTGAAAGCAG
1 TAGATAATATATAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAG
*
262511 TAGATAATATATTAATATACAACTGATTGATAATAATTATCTTATTTGAAAGCAG
1 TAGATAATATA-TAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAG
262566 TAGATAA
1 TAGATAA
262573 CTCAAGTATG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 10 0.18
55 47 0.82
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (54 bp):
TAGATAATATATAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAG
Found at i:268208 original size:36 final size:36
Alignment explanation
Indices: 268168--268240 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
268158 AAATATATTA
268168 TAATTAAATTATGATATCATCATTGTTATATACATT
1 TAATTAAATTATGATATCATCATTGTTATATACATT
* *
268204 TAATTGAATTATGATATCATCATTGTTATATATATT
1 TAATTAAATTATGATATCATCATTGTTATATACATT
268240 T
1 T
268241 TATGATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (36 bp):
TAATTAAATTATGATATCATCATTGTTATATACATT
Found at i:269382 original size:28 final size:26
Alignment explanation
Indices: 269351--269408 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
269341 GATTTGGACC
* * *
269351 CACTGTTTTGCGTTCATTTTTATTTAA
1 CACTGATTTACGTT-ATTTTTAATTAA
*
269378 TCACTGATTTACGTTTTTTTTAATTAA
1 -CACTGATTTACGTTATTTTTAATTAA
269405 CACT
1 CACT
269409 AACATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 10 0.38
28 12 0.46
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (26 bp):
CACTGATTTACGTTATTTTTAATTAA
Found at i:271713 original size:23 final size:23
Alignment explanation
Indices: 271687--271731 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
271677 CACCACAGCT
*
271687 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
271710 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
271732 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:271904 original size:150 final size:149
Alignment explanation
Indices: 271699--272014 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
271689 TATAAATGCA
*
271699 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
271763 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* * *
271828 TTCACATAATATATATATATC
129 TTCAAAGAATATACATATATC
271849 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
271914 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTT
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTT
*
271979 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
271998 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
272015 CCCTCTACCC
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTT
CAAAGAATATACATATATC
Found at i:272527 original size:19 final size:20
Alignment explanation
Indices: 272490--272527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
272480 TTTTTTCTCA
*
272490 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
272510 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
272528 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:278673 original size:23 final size:23
Alignment explanation
Indices: 278647--278691 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
278637 CACCACAGCT
*
278647 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
278670 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
278692 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:278859 original size:150 final size:149
Alignment explanation
Indices: 278659--278974 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
278649 TATAAATGCA
*
278659 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
278723 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* * *
278788 TCCACATAATATATATATATC
129 TCCAAAGAATATACATATATC
278809 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
278874 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
278939 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
278958 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
278975 CCCTCTACCC
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:281233 original size:110 final size:110
Alignment explanation
Indices: 281040--281258 Score: 429
Period size: 110 Copynumber: 2.0 Consensus size: 110
281030 TCAATAAAAA
281040 TATTTGTTTGTATCATTTAATTTTTTTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGT
1 TATTTGTTTGTATCATTTAATTTTTTTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGT
281105 ATGATCCTATTTGACTCCTTAGTAGTTAGTTTTTGTATTGTAATT
66 ATGATCCTATTTGACTCCTTAGTAGTTAGTTTTTGTATTGTAATT
*
281150 TATTTGTTTGTATCATTTATTTTTTTTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGT
1 TATTTGTTTGTATCATTTAATTTTTTTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGT
281215 ATGATCCTATTTGACTCCTTAGTAGTTAGTTTTTGTATTGTAAT
66 ATGATCCTATTTGACTCCTTAGTAGTTAGTTTTTGTATTGTAAT
281259 GATTGTAAAG
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (110 bp):
TATTTGTTTGTATCATTTAATTTTTTTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGT
ATGATCCTATTTGACTCCTTAGTAGTTAGTTTTTGTATTGTAATT
Found at i:281308 original size:110 final size:108
Alignment explanation
Indices: 281065--281309 Score: 237
Period size: 110 Copynumber: 2.2 Consensus size: 108
281055 TTTAATTTTT
**
281065 TTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGTATGATCCTATTTGACTCCTTAGTAG
1 TTCAAATTATTTAATT--GTTTTTAATCTTATCCTATTGTATGATCCTATTTGACTCCTTAGTAG
* ** * *** **
281130 TTAGTTTTTGTATTGTAATTTATTTGTTTGTATCATTTATTTTTT
64 TTAGTTTTTGTATTGTAATTGATTTGGGTGTATCAGTTAACATGA
**
281175 TTCAAATTATTTGGTTGAGTTTTTAATCTTATCCTATTGTATGATCCTATTTGACTCCTTAGTAG
1 TTCAAATTATTTAATT--GTTTTTAATCTTATCCTATTGTATGATCCTATTTGACTCCTTAGTAG
*
281240 TTAGTTTTTGTATTGTAA-TGATTGTAAAGGG-GTGATTAGTTAACATGA
64 TTAGTTTTTGTATTGTAATTGATT-T---GGGTGT-ATCAGTTAACATGA
*
281288 TT-AATTTACTTTAATT-TTTTTA
1 TTCAAATTA-TTTAATTGTTTTTA
281310 TATTTCTTAT
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
109 4 0.03
110 90 0.78
112 7 0.06
113 15 0.13
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (108 bp):
TTCAAATTATTTAATTGTTTTTAATCTTATCCTATTGTATGATCCTATTTGACTCCTTAGTAGTT
AGTTTTTGTATTGTAATTGATTTGGGTGTATCAGTTAACATGA
Found at i:281863 original size:21 final size:22
Alignment explanation
Indices: 281839--281879 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
281829 GATTTGTGCT
281839 GCAAAGTG-AGCAATAATTCAC
1 GCAAAGTGAAGCAATAATTCAC
281860 GCAAAGTGAAGCAATAATTC
1 GCAAAGTGAAGCAATAATTC
281880 GGGTGGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
GCAAAGTGAAGCAATAATTCAC
Found at i:282044 original size:26 final size:26
Alignment explanation
Indices: 282008--282059 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
281998 TCGGTTGTAA
* *
282008 GAAGAAGAAAGAAGGGTGAAGGAAAG
1 GAAGAAAAAAGAAAGGTGAAGGAAAG
282034 GAAGAAAAAAGAAAGGTGAAGGAAAG
1 GAAGAAAAAAGAAAGGTGAAGGAAAG
282060 AAAGGTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (26 bp):
GAAGAAAAAAGAAAGGTGAAGGAAAG
Found at i:283031 original size:18 final size:18
Alignment explanation
Indices: 283008--283043 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
282998 GGTAAAACCA
283008 GAGTGTAAAGGGTGGCGT
1 GAGTGTAAAGGGTGGCGT
283026 GAGTGTAAAGGGTGGCGT
1 GAGTGTAAAGGGTGGCGT
283044 CTCAAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.50, T:0.22
Consensus pattern (18 bp):
GAGTGTAAAGGGTGGCGT
Found at i:284775 original size:21 final size:23
Alignment explanation
Indices: 284722--284779 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
284712 TAAATTTTAT
284722 TTAAATA-TATT--TAATCATTA
1 TTAAATAGTATTAGTAATCATTA
*
284742 TTAAATTATTATTAGTAATCATTA
1 TTAAA-TAGTATTAGTAATCATTA
284766 TT-AA-AGTATTAGTA
1 TTAAATAGTATTAGTA
284780 TCAAATCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 5 0.15
21 11 0.33
22 4 0.12
23 2 0.06
24 11 0.33
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAAATAGTATTAGTAATCATTA
Found at i:284776 original size:27 final size:27
Alignment explanation
Indices: 284733--284954 Score: 239
Period size: 27 Copynumber: 8.3 Consensus size: 27
284723 TAAATATATT
*
284733 TAATCATTATTA-AA-TT-ATTATTAG
1 TAATCATTATTATAATTTCATTATTAC
* *
284757 TAATCATTATTA-AA-GT-ATTAGTATC
1 TAATCATTATTATAATTTCATTATTA-C
*
284782 AAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
*
284809 TAATCATTACTA-AA--TCATTAATATA-
1 TAATCATTATTATAATTTCATT-AT-TAC
*
284834 AAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
284861 TAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
*
284888 TAATCATTATTATAATTTCATCATTAGTATC
1 TAATCATTATTATAA-TT--TCATTATTA-C
*
284919 AAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
284946 TAATCATTA
1 TAATCATTA
284955 CTAAATCAAC
Statistics
Matches: 169, Mismatches: 15, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
24 26 0.15
25 23 0.14
26 10 0.06
27 64 0.38
28 21 0.12
30 10 0.06
31 15 0.09
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATCATTATTATAATTTCATTATTAC
Found at i:284802 original size:14 final size:14
Alignment explanation
Indices: 284785--284949 Score: 141
Period size: 14 Copynumber: 11.9 Consensus size: 14
284775 TAGTATCAAA
284785 TCATTATTATAATT
1 TCATTATTATAATT
284799 TCATTATTACTAA--
1 TCATTATTA-TAATT
*
284812 TCATTACTA-AA--
1 TCATTATTATAATT
* **
284823 TCATTAATATAAAA
1 TCATTATTATAATT
284837 TCATTATTATAATT
1 TCATTATTATAATT
284851 TCATTATTACTAA--
1 TCATTATTA-TAATT
284864 TCATTATTATAATT
1 TCATTATTATAATT
284878 TCATTATTACTAA--
1 TCATTATTA-TAATT
284891 TCATTATTATAATT
1 TCATTATTATAATT
* **
284905 TCATCATTAGTATCAAA
1 TCATTATTA-TA--ATT
284922 TCATTATTATAATT
1 TCATTATTATAATT
284936 TCATTATTACTAAT
1 TCATTATTA-TAAT
284950 CATTACTAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
11 10 0.08
12 8 0.06
13 26 0.21
14 56 0.44
15 15 0.12
16 2 0.02
17 9 0.07
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (14 bp):
TCATTATTATAATT
Found at i:284813 original size:52 final size:52
Alignment explanation
Indices: 284734--284913 Score: 226
Period size: 52 Copynumber: 3.5 Consensus size: 52
284724 AAATATATTT
* *
284734 AATCATTATTA-AA-TT-ATTATTAGTAATCATTATTAAAGT-ATTAGTATCA
1 AATCATTATTATAATTTCATTATTACTAATCATTATTAAA-TCATTAATATCA
* *
284783 AATCATTATTATAATTTCATTATTACTAATCATTACTAAATCATTAATATAA
1 AATCATTATTATAATTTCATTATTACTAATCATTATTAAATCATTAATATCA
* *
284835 AATCATTATTATAATTTCATTATTACTAATCATTATTATAATTTCATTATTA-CT
1 AATCATTATTATAATTTCATTATTACTAATCATTATTA-AA--TCATTAATATCA
*
284889 AATCATTATTATAATTTCATCATTA
1 AATCATTATTATAATTTCATTATTA
284914 GTATCAAATC
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
49 11 0.10
50 2 0.02
51 3 0.03
52 65 0.57
53 2 0.02
54 24 0.21
55 8 0.07
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (52 bp):
AATCATTATTATAATTTCATTATTACTAATCATTATTAAATCATTAATATCA
Found at i:284912 original size:17 final size:17
Alignment explanation
Indices: 284890--284944 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
284880 ATTATTACTA
284890 ATCATTATTATAATTTC
1 ATCATTATTATAATTTC
*
284907 ATCATTAGTATCAA----
1 ATCATTATTAT-AATTTC
284921 ATCATTATTATAATTTC
1 ATCATTATTATAATTTC
*
284938 ATTATTA
1 ATCATTA
284945 CTAATCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
17 16 0.53
18 2 0.07
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (17 bp):
ATCATTATTATAATTTC
Found at i:284939 original size:58 final size:54
Alignment explanation
Indices: 284783--284954 Score: 208
Period size: 52 Copynumber: 3.1 Consensus size: 54
284773 ATTAGTATCA
* * * *
284783 AATCATTATTATAATTTCATTATTACTAATCATTACTA-AA--TCATTAATATA-A
1 AATCATTATTATAATTTCATTAGTACAAATCATTATTATAATTTCATT-AT-TACT
* *
284835 AATCATTATTATAATTTCATTATTACTAATCATTATTATAATTTCATTATTACT
1 AATCATTATTATAATTTCATTAGTACAAATCATTATTATAATTTCATTATTACT
284889 AATCATTATTATAATTTCATCATTAGTATCAAATCATTATTATAATTTCATTATTACT
1 AATCATTATTATAA-TT--TCATTAGTA-CAAATCATTATTATAATTTCATTATTACT
284947 AATCATTA
1 AATCATTA
284955 CTAAATCAAC
Statistics
Matches: 108, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
52 37 0.34
53 4 0.04
54 16 0.15
55 7 0.06
57 8 0.07
58 36 0.33
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.48
Consensus pattern (54 bp):
AATCATTATTATAATTTCATTAGTACAAATCATTATTATAATTTCATTATTACT
Found at i:284946 original size:85 final size:79
Alignment explanation
Indices: 284783--284954 Score: 263
Period size: 85 Copynumber: 2.1 Consensus size: 79
284773 ATTAGTATCA
*
284783 AATCATTATTATAATTTCATTATTACTAATCATTACTAAATCATTAATATAAAATCATTATTATA
1 AATCATTATTATAATTTCATTATTACTAATCATTAATAAATCATTAATATAAAATCATTATTATA
284848 ATTTCATTATTACT
66 ATTTCATTATTACT
* *
284862 AATCATTATTATAATTTCATTATTACTAATCATTATTATAATTTCATCATTAGTATCAAATCATT
1 AATCATTATTATAATTTCATTATTACTAATCATTA--ATAA----ATCATTAATATAAAATCATT
284927 ATTATAATTTCATTATTACT
60 ATTATAATTTCATTATTACT
284947 AATCATTA
1 AATCATTA
284955 CTAAATCAAC
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
79 35 0.42
81 3 0.04
85 46 0.55
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.48
Consensus pattern (79 bp):
AATCATTATTATAATTTCATTATTACTAATCATTAATAAATCATTAATATAAAATCATTATTATA
ATTTCATTATTACT
Found at i:287298 original size:28 final size:31
Alignment explanation
Indices: 287238--287303 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
287228 TCATATAATA
287238 TAATATCATATATAACTTAAACTAACAAACAAAC
1 TAATATCATATATAACTTAAACT---AAACAAAC
287272 TAATAT-A-ATATAACTTAAACT-AACAAAC
1 TAATATCATATATAACTTAAACTAAACAAAC
287300 TAAT
1 TAAT
287304 GATTTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 11 0.34
32 14 0.44
33 1 0.03
34 6 0.19
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (31 bp):
TAATATCATATATAACTTAAACTAAACAAAC
Found at i:287369 original size:25 final size:27
Alignment explanation
Indices: 287331--287381 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
287321 TTTTACCCGG
287331 TCTCTTCTTATCCCTTTC-TTCTTCTT
1 TCTCTTCTTATCCCTTTCTTTCTTCTT
*
287357 TCTC-TCTTCTCCCTTTCTTTCTTCT
1 TCTCTTCTTATCCCTTTCTTTCTTCT
287382 CCCTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (27 bp):
TCTCTTCTTATCCCTTTCTTTCTTCTT
Found at i:287374 original size:15 final size:15
Alignment explanation
Indices: 287344--287395 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
287334 CTTCTTATCC
*
287344 CTTTCTTCT-TCTTT
1 CTTTCTTCTCCCTTT
*
287358 CTCTCTTCTCCCTTT
1 CTTTCTTCTCCCTTT
287373 CTTTCTTCTCCCTTT
1 CTTTCTTCTCCCTTT
287388 CTTTCTTC
1 CTTTCTTC
287396 ATAACCGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 8 0.24
15 26 0.76
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTCTTCTCCCTTT
Found at i:287949 original size:30 final size:31
Alignment explanation
Indices: 287879--287962 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 31
287869 CACTATAAGG
*
287879 TCGCCCCGACTGCATGGCGACCTACAAGGGCT
1 TCGCCCCGACTGCATGGCGACCTACAA-GGAT
**
287911 TCGCCCCGACTGCATGGCGACCTTTAA-GAT
1 TCGCCCCGACTGCATGGCGACCTACAAGGAT
* * *
287941 TTGCCCCGACTGTATGGTGACC
1 TCGCCCCGACTGCATGGCGACC
287963 AATCTTACCC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 21 0.46
32 25 0.54
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (31 bp):
TCGCCCCGACTGCATGGCGACCTACAAGGAT
Found at i:289715 original size:31 final size:31
Alignment explanation
Indices: 289680--289742 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
289670 ACGAATTCGA
289680 GATGTCCAAGCATGGAAGCAACGTGCAATGG
1 GATGTCCAAGCATGGAAGCAACGTGCAATGG
289711 GATGTCCAAGCATGGAAGCAACGTGCAATGG
1 GATGTCCAAGCATGGAAGCAACGTGCAATGG
289742 G
1 G
289743 GTTTCAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.33, T:0.16
Consensus pattern (31 bp):
GATGTCCAAGCATGGAAGCAACGTGCAATGG
Found at i:290656 original size:33 final size:34
Alignment explanation
Indices: 290619--290689 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
290609 CCTTTACAAC
*
290619 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
290652 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
290686 TCCC
1 TCCC
290690 ATTTACAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:291327 original size:21 final size:21
Alignment explanation
Indices: 291303--291342 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
291293 ATGTTTAATG
291303 AAAAAGATA-CTAATTGTTAAC
1 AAAAAGATATC-AATTGTTAAC
*
291324 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
291343 CCAAGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:292925 original size:15 final size:15
Alignment explanation
Indices: 292905--292955 Score: 102
Period size: 15 Copynumber: 3.4 Consensus size: 15
292895 GTTTTTCTCC
292905 TCTTCCCTTTCTTCA
1 TCTTCCCTTTCTTCA
292920 TCTTCCCTTTCTTCA
1 TCTTCCCTTTCTTCA
292935 TCTTCCCTTTCTTCA
1 TCTTCCCTTTCTTCA
292950 TCTTCC
1 TCTTCC
292956 TTCACCATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTCCCTTTCTTCA
Found at i:293992 original size:34 final size:33
Alignment explanation
Indices: 293931--294001 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
293921 CCTTTACAAC
*
293931 TCCCTAGTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGATAAACTAGAACCTT
* * *
293964 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAG-TTTTACACGGGATAAACTAGAACCTT
293998 TCCC
1 TCCC
294002 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGATAAACTAGAACCTT
Found at i:294241 original size:20 final size:22
Alignment explanation
Indices: 294216--294255 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
294206 AGTCGTATAT
294216 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
294236 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
294256 TATACAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:295274 original size:15 final size:16
Alignment explanation
Indices: 295249--295282 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
295239 AATATTCTAA
295249 ACTGAGTAGTATCGAT
1 ACTGAGTAGTATCGAT
*
295265 ACTG-GTAGTATCGGT
1 ACTGAGTAGTATCGAT
295280 ACT
1 ACT
295283 ACCCAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (16 bp):
ACTGAGTAGTATCGAT
Found at i:299649 original size:21 final size:21
Alignment explanation
Indices: 299607--299649 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
299597 TTTCTGGGCT
* *
299607 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
299628 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
299649 A
1 A
299650 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:300524 original size:103 final size:103
Alignment explanation
Indices: 300196--300516 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
300186 GTAGAGGGTC
300196 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
300261 TTGATCATTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
300299 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
300364 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
300402 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
300467 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
300505 TATGTGGTCCTT
1 TATGTGGTCCTT
300517 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:300594 original size:23 final size:23
Alignment explanation
Indices: 300532--300595 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
300522 CATTATTATA
300532 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* * ** *
300555 CGGTACTCCGGTACAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
300578 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
300596 ATATGACCTG
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:306680 original size:21 final size:21
Alignment explanation
Indices: 306638--306680 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
306628 TTTATGGGCT
* *
306638 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
306659 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
306680 A
1 A
306681 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:306733 original size:20 final size:20
Alignment explanation
Indices: 306708--306745 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
306698 GAATGCTAGA
306708 GGGGAATCGATACCCCCAGG
1 GGGGAATCGATACCCCCAGG
*
306728 GGGGAATCGATTCCCCCA
1 GGGGAATCGATACCCCCA
306746 TAATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGAATCGATACCCCCAGG
Found at i:307408 original size:103 final size:103
Alignment explanation
Indices: 307224--307544 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
307214 GTAGAGGGTC
307224 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
307289 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
307327 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
307392 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
307430 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
307495 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
307533 TATGTGGTCCTT
1 TATGTGGTCCTT
307545 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:307594 original size:23 final size:23
Alignment explanation
Indices: 307561--307623 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
307551 ATTATTATAT
307561 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
307584 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
307607 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
307624 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:325167 original size:18 final size:18
Alignment explanation
Indices: 325140--325186 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
325130 TACAAATACA
325140 CACACACACACTCACACT
1 CACACACACACTCACACT
*
325158 CACACTCACACTCACACT
1 CACACACACACTCACACT
325176 CACACACACAC
1 CACACACACAC
325187 ACATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.51, G:0.00, T:0.11
Consensus pattern (18 bp):
CACACACACACTCACACT
Found at i:325189 original size:6 final size:6
Alignment explanation
Indices: 325140--325186 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
325130 TACAAATACA
* *
325140 CACACA CACACT CACACT CACACT CACACT CACACT CACACA CACAC
1 CACACT CACACT CACACT CACACT CACACT CACACT CACACT CACAC
325187 ACATATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.38, C:0.51, G:0.00, T:0.11
Consensus pattern (6 bp):
CACACT
Found at i:328509 original size:21 final size:20
Alignment explanation
Indices: 328423--328580 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
328413 AAATGATCAA
**
328423 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
328442 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
328462 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
328482 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
328503 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
328524 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
328544 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
328565 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
328581 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:328609 original size:20 final size:20
Alignment explanation
Indices: 328547--328699 Score: 191
Period size: 20 Copynumber: 7.7 Consensus size: 20
328537 CGATTTTACA
* ** *
328547 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
328567 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
328587 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
328607 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
328627 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
328647 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
328667 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
328687 AAATCGCAACGCG
1 AAATCGCAACGCG
328700 ATATTTAAAG
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 111 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:329121 original size:33 final size:33
Alignment explanation
Indices: 329082--329152 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
329072 TTCACTTAGA
* *
329082 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
329115 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
329148 TTTCA
1 TTTCA
329153 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:329258 original size:21 final size:20
Alignment explanation
Indices: 329232--329337 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
329222 TGCAGAAGAG
329232 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
329253 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
329273 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
329294 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
329308 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
329327 TCGCAACGAGA
1 TCGCAACGAGA
329338 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:329276 original size:20 final size:21
Alignment explanation
Indices: 329230--329308 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
329220 TTTGCAGAAG
*
329230 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
329252 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
329271 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
329293 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
329309 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:329289 original size:41 final size:38
Alignment explanation
Indices: 329225--329341 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
329215 TTCAATTTGC
* *
329225 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
329263 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
329304 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
329337 AGAAT
1 AGAAT
329342 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:329314 original size:14 final size:14
Alignment explanation
Indices: 329295--329348 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
329285 AAATGAAAAG
329295 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
329309 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
329328 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
329342 CGCAACG
1 CGCAACG
329349 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:329324 original size:33 final size:33
Alignment explanation
Indices: 329284--329353 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
329274 CGCAACGAGA
329284 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
329317 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
329350 GAAA
1 GAAA
329354 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:329360 original size:33 final size:33
Alignment explanation
Indices: 329290--329364 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
329280 GAGAGAAATG
* **
329290 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
329323 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
329356 AAAATCGCA
1 AAAATCGCA
329365 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:329382 original size:19 final size:19
Alignment explanation
Indices: 329360--329457 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
329350 GAAACCAAAA
*
329360 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
329379 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
329393 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
329412 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
329426 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
329445 TCGCGTTGCGATT
1 TCGCGTTGCGATT
329458 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:329401 original size:14 final size:14
Alignment explanation
Indices: 329382--329471 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
329372 TTTCATTTCG
329382 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
329396 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
329415 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
329429 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
329446 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
329462 CGTTGCGATT
1 CGTTGCGATT
329472 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:329407 original size:33 final size:33
Alignment explanation
Indices: 329365--329479 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
329355 CAAAATCGCA
329365 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
329398 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
329431 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
329464 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
329480 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:331485 original size:183 final size:183
Alignment explanation
Indices: 331178--331555 Score: 697
Period size: 183 Copynumber: 2.1 Consensus size: 183
331168 TAGATTGCTT
*
331178 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTTTAACACTGTGAAATAGTATT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTATAACACTGTGAAATAGTATT
331243 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
331308 GTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
331360 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTATAACACTGTGAAATAGTA
331425 TTTGTCTTT-TTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
331489 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 GTGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
331545 AGTAAATTTAT
1 AGTAAATTTAT
331556 CCATTCAAGT
Statistics
Matches: 189, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
182 35 0.19
183 71 0.38
184 35 0.19
185 48 0.25
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATTCTATAACACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:331496 original size:92 final size:93
Alignment explanation
Indices: 331178--331553 Score: 699
Period size: 91 Copynumber: 4.1 Consensus size: 93
331168 TAGATTGCTT
*
331178 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331241 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
331269 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331332 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
331360 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331425 TTTGTCTTT-TTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
331452 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
331517 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
331545 AGTAAATTT
1 AGTAAATTT
331554 ATCCATTCAA
Statistics
Matches: 277, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
91 125 0.45
92 91 0.33
93 61 0.22
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:331637 original size:19 final size:19
Alignment explanation
Indices: 331597--331725 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
331587 TAGTTTACTT
* *
331597 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
331617 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
331636 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
331655 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
331669 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
331688 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
331702 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
331721 TCGCA
1 TCGCA
331726 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:331676 original size:33 final size:32
Alignment explanation
Indices: 331633--331725 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
331623 CGCGAAACCA
**
331633 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
331665 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
331698 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
331726 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:331723 original size:52 final size:52
Alignment explanation
Indices: 331597--331725 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
331587 TAGTTTACTT
**
331597 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
331649 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
331702 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
331726 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:331743 original size:19 final size:19
Alignment explanation
Indices: 331721--331855 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
331711 GAAACCAAAA
*
331721 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
331740 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
331756 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
331773 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
331789 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
331806 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
331825 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
331845 TCGTGTTGCGA
1 TCGCGTTGCGA
331856 AAGTAACTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:331762 original size:14 final size:14
Alignment explanation
Indices: 331743--331799 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
331733 TTTCATTTCG
331743 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
331757 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
331774 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
331790 CGTTGCGATT
1 CGTTGCGATT
331800 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:331768 original size:33 final size:33
Alignment explanation
Indices: 331726--331818 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
331716 CAAAATCGCA
*
331726 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
331759 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
331792 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
331819 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:333800 original size:14 final size:14
Alignment explanation
Indices: 333781--333816 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
333771 ATTGTTTAAT
333781 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
333795 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
333809 TGATTTGT
1 TGATTTGT
333817 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:333947 original size:19 final size:19
Alignment explanation
Indices: 333923--334020 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
333913 AAAATTGACT
333923 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
333942 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
333961 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
333975 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
333994 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
334014 ATCGCAA
1 ATCGCAA
334021 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:334052 original size:53 final size:53
Alignment explanation
Indices: 333923--334039 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
333913 AAAATTGACT
333923 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
333975 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
334028 ATCGCAATGCGA
1 ATCGCAATGCGA
334040 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:336372 original size:12 final size:12
Alignment explanation
Indices: 336355--336379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
336345 TCTTCGGGGA
336355 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336367 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336379 C
1 C
336380 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:336588 original size:24 final size:24
Alignment explanation
Indices: 336554--336600 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
336544 CTGAAACATC
336554 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
336578 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
336601 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:337311 original size:20 final size:20
Alignment explanation
Indices: 337283--337512 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
337273 AAATTTCAGT
* * *
337283 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
337303 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
337323 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
337343 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
337363 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
337383 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
337403 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
337423 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
337443 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
337463 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
337483 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
337503 GTTGCGATTT
1 GTTGCGATTT
337513 TGGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:337529 original size:21 final size:21
Alignment explanation
Indices: 337499--337581 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
337489 ATTTTCATAT
*
337499 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
337520 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
337541 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
337562 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
337582 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:337572 original size:42 final size:43
Alignment explanation
Indices: 337479--337577 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
337469 ATTTATGTGT
* *
337479 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
337520 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
337562 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
337578 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:346325 original size:2 final size:2
Alignment explanation
Indices: 346318--346343 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
346308 TATTTAAATA
346318 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
346344 TAATACACGC
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):
AT
Found at i:357213 original size:23 final size:24
Alignment explanation
Indices: 357167--357220 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
357157 CAATGATTAA
*
357167 ATGTAAATTAACATAGTTTAATTT
1 ATGTAAATTAACATAATTTAATTT
*
357191 ATGTAAATT-ATATAATTTAATTT
1 ATGTAAATTAACATAATTTAATTT
357214 ATGTAAA
1 ATGTAAA
357221 GAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
ATGTAAATTAACATAATTTAATTT
Found at i:357808 original size:18 final size:17
Alignment explanation
Indices: 357775--357809 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
357765 AAATTACAAG
357775 GCAACAACAGGCAACAT
1 GCAACAACAGGCAACAT
*
357792 GCAACAGACATGCAACAT
1 GCAACA-ACAGGCAACAT
357810 TTCTGCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (17 bp):
GCAACAACAGGCAACAT
Found at i:361620 original size:20 final size:20
Alignment explanation
Indices: 361595--361633 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
361585 TTCATCCTTA
361595 TATAATTTATATTAATAAAC
1 TATAATTTATATTAATAAAC
361615 TATAATTTATATTAATAAA
1 TATAATTTATATTAATAAA
361634 TTATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATTTATATTAATAAAC
Found at i:361683 original size:9 final size:9
Alignment explanation
Indices: 361594--361723 Score: 52
Period size: 9 Copynumber: 15.4 Consensus size: 9
361584 TTTCATCCTT
*
361594 ATATAATTT
1 ATATAATTA
*
361603 ATATTAATAA
1 ATA-TAATTA
361613 ACTATAATT-
1 A-TATAATTA
361622 -TAT-ATTA
1 ATATAATTA
361629 ATA-AATT-
1 ATATAATTA
*
361636 ATTTAATTA
1 ATATAATTA
* *
361645 ATAGAGTTA
1 ATATAATTA
361654 ATATAA--A
1 ATATAATTA
* *
361661 CTATCATT-
1 ATATAATTA
361669 -TATAATTA
1 ATATAATTA
361677 ATATAATATA
1 ATATAAT-TA
*
361687 A-ATTATATA
1 ATATAAT-TA
*
361696 TTATAATT-
1 ATATAATTA
361704 A-AT-ATTA
1 ATATAATTA
361711 ATATAATTA
1 ATATAATTA
361720 ATAT
1 ATAT
361724 TAATATTAAC
Statistics
Matches: 89, Mismatches: 16, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
6 6 0.07
7 19 0.21
8 11 0.12
9 35 0.39
10 16 0.18
11 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (9 bp):
ATATAATTA
Found at i:361710 original size:6 final size:6
Alignment explanation
Indices: 361673--361745 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
361663 ATCATTTATA
361673 ATTAAT A-TAAT A-TAA- ATTATAT ATT-AT AATTAAT ATTAAT A-T-A-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT
*
361716 ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
361746 AATTTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 18 0.33
6 27 0.49
7 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:361741 original size:16 final size:16
Alignment explanation
Indices: 361671--361779 Score: 88
Period size: 15 Copynumber: 7.0 Consensus size: 16
361661 CTATCATTTA
361671 TAATTAATA-TAATAT
1 TAATTAATATTAATAT
* *
361686 AAATT-ATA-TATTA-
1 TAATTAATATTAATAT
361699 TAATTAATATTAATA-
1 TAATTAATATTAATAT
361714 TAATTAATATTAATAT
1 TAATTAATATTAATAT
361730 TAACTT-ATATTAATA-
1 TAA-TTAATATTAATAT
* * *
361745 TAATTTAGTTTATAATTT
1 TAA-TTAATAT-TAATAT
361763 GTAATTAATATTAATAT
1 -TAATTAATATTAATAT
361780 AAAATATAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
13 4 0.05
14 10 0.13
15 28 0.37
16 14 0.19
17 11 0.15
18 5 0.07
19 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTAATATTAATAT
Found at i:361743 original size:31 final size:30
Alignment explanation
Indices: 361615--361877 Score: 140
Period size: 31 Copynumber: 8.6 Consensus size: 30
361605 ATTAATAAAC
*
361615 TATAATTTATATT-A-ATAAATTAT-TTAA
1 TATAATTAATATTAATATAAATTATATTAA
* *
361642 T-TAA-TAGA-GTTAATATAAACTATCATT--
1 TATAATTA-ATATTAATATAAATTAT-ATTAA
*
361669 TATAATTAATA-TAATATAAATTATA-TAT
1 TATAATTAATATTAATATAAATTATATTAA
361697 TATAATTAATATTAATAT-AATTAATATTAA
1 TATAATTAATATTAATATAAATT-ATATTAA
* *
361727 TATTAACTT-ATATTAATATAATTTAGTTTATAA
1 TA-TAA-TTAATATTAATATAAATTA-TAT-TAA
* *
361760 TTTGTAATTAATATTAATATAAAATATAGTCT-A
1 --TATAATTAATATTAATATAAATTATA-T-TAA
* * *
361793 TAAAATTAATATTAATATAAACTATATT-T
1 TATAATTAATATTAATATAAATTATATTAA
* * *
361822 TATAAATTATATAGTAGAGTTTATAAACTACAGTTAA
1 TAT-AATTA-ATATTA-A---TATAAATTATA-TTAA
361859 TATAATTAATATTAATATA
1 TATAATTAATATTAATATA
361878 GTATATGGTT
Statistics
Matches: 184, Mismatches: 22, Indels: 56
0.70 0.08 0.21
Matches are distributed among these distances:
25 3 0.02
26 6 0.03
27 11 0.06
28 31 0.17
29 16 0.09
30 10 0.05
31 46 0.25
32 8 0.04
33 7 0.04
34 20 0.11
35 16 0.09
36 7 0.04
37 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
TATAATTAATATTAATATAAATTATATTAA
Found at i:361817 original size:24 final size:25
Alignment explanation
Indices: 361772--361818 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
361762 TGTAATTAAT
**
361772 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
361797 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
361819 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:362005 original size:36 final size:36
Alignment explanation
Indices: 361965--362043 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
361955 TAATGTAAAC
*
361965 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
* *
362001 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
362037 TATAGTT
1 TATAGTT
362044 AAGATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Found at i:362040 original size:15 final size:15
Alignment explanation
Indices: 362022--362072 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
362012 AACTATATAC
362022 TATATTAATATAAAT
1 TATATTAATATAAAT
*
362037 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
362052 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
362068 TATAT
1 TATAT
362073 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:362095 original size:20 final size:21
Alignment explanation
Indices: 362054--362095 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
362044 AAGATAATTA
362054 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
362076 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
362096 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:362112 original size:21 final size:21
Alignment explanation
Indices: 362083--362130 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
362073 AGTACATTAA
* *
362083 TATAAACTATAGTTTATAAAT
1 TATATACTATAGGTTATAAAT
362104 TATATACTATAGGTTATAAAT
1 TATATACTATAGGTTATAAAT
362125 TATATA
1 TATATA
362131 GTACACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (21 bp):
TATATACTATAGGTTATAAAT
Found at i:362242 original size:13 final size:13
Alignment explanation
Indices: 362220--362253 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
362210 TACATAATAC
362220 ACATACTATAGGTT
1 ACATA-TATAGGTT
*
362234 ACATATATAGTTT
1 ACATATATAGGTT
362247 ACATATA
1 ACATATA
362254 AATAGATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (13 bp):
ACATATATAGGTT
Found at i:362282 original size:24 final size:23
Alignment explanation
Indices: 362246--362294 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
362236 ATATATAGTT
362246 TACATATAAATAGATTGTATATA
1 TACATATAAATAGATTGTATATA
* * *
362269 TACATATACTATAGGTTTTATATA
1 TACATATA-AATAGATTGTATATA
362293 TA
1 TA
362295 GTTTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (23 bp):
TACATATAAATAGATTGTATATA
Found at i:362330 original size:20 final size:20
Alignment explanation
Indices: 362284--362334 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
362274 ATACTATAGG
*
362284 TTTTATATATAGTTTATATA
1 TTTTATACATAGTTTATATA
**
362304 TACTATACATAGTTTATA-A
1 TTTTATACATAGTTTATATA
362323 CTTTTATACATA
1 -TTTTATACATA
362335 CATGTACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTATACATAGTTTATATA
Found at i:362557 original size:17 final size:19
Alignment explanation
Indices: 362535--362807 Score: 125
Period size: 18 Copynumber: 14.0 Consensus size: 19
362525 TTCTATAAAC
*
362535 TATATATTTTAT-TAT-TT
1 TATATATTTTATATATATA
362552 TATATAGTTTATATATATATA
1 TATATA-TTT-TATATATATA
*
362573 TATATATATATATATATATA
1 TATATAT-TTTATATATATA
* * *
362593 TATATAATCTATAGAT-TA
1 TATATATTTTATATATATA
*
362611 CATATATTACTTATACATATATA
1 TATATATT--TTAT--ATATATA
* *
362634 TATACTATATTA-ATATAAA
1 TATA-TATTTTATATATATA
*
362653 T-TATAATTTATA-A-ACTA
1 TATATATTTTATATATA-TA
* * *
362670 TA-ACTGATGTATAGTTTATACA
1 TATA-T-AT-TTTA-TATATATA
* *
362692 TATATAGTTTATATACATA
1 TATATATTTTATATATATA
*
362711 TATATA-TATATATATATA
1 TATATATTTTATATATATA
*
362729 TATATA-TATATATATATA
1 TATATATTTTATATATATA
* * *
362747 TATATATTATAGTTTATAAA
1 TATATATTTTA-TATATATA
*
362767 CTATATACTTTTATAGTTTATA
1 -TATATA-TTTTATA-TATATA
* *
362789 TACATAGTTTATATATATA
1 TATATATTTTATATATATA
362808 ATTCATATAA
Statistics
Matches: 195, Mismatches: 35, Indels: 50
0.70 0.12 0.18
Matches are distributed among these distances:
16 1 0.01
17 15 0.08
18 49 0.25
19 38 0.19
20 41 0.21
21 22 0.11
22 19 0.10
23 7 0.04
24 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (19 bp):
TATATATTTTATATATATA
Found at i:362564 original size:9 final size:9
Alignment explanation
Indices: 362535--362597 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 9
362525 TTCTATAAAC
362535 TATATATTT
1 TATATATTT
362544 TAT-TATTT
1 TATATATTT
*
362552 TATATAGTT
1 TATATATTT
*
362561 TATATATATA
1 TATATAT-TT
*
362571 TATATATATA
1 TATATAT-TT
*
362581 TATATATATA
1 TATATAT-TT
362591 TATATAT
1 TATATAT
362598 AATCTATAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
8 8 0.16
9 13 0.27
10 28 0.57
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATATATTT
Found at i:362566 original size:2 final size:2
Alignment explanation
Indices: 362561--362757 Score: 153
Period size: 2 Copynumber: 100.0 Consensus size: 2
362551 TTATATAGTT
*
362561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
362602 TA TA GA T- TA CA TA TA T- TA CT- TA TA CA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
* * * *
362643 T- TA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA -A CTGA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -T-A TA TA
* * * *
362681 TA GTT TA TA CA TA TA TA GTT TA TA TA CA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
362725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362758 GTTTATAAAC
Statistics
Matches: 154, Mismatches: 24, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
1 10 0.06
2 136 0.88
3 7 0.05
4 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:362803 original size:15 final size:15
Alignment explanation
Indices: 362785--362832 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
362775 TTTTATAGTT
362785 TATATACATAGTTTA
1 TATATACATAGTTTA
* *
362800 TATAT--ATAATTCA
1 TATATACATAGTTTA
*
362813 TATAAACATAGTTTA
1 TATATACATAGTTTA
362828 TATAT
1 TATAT
362833 GTAGCTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (15 bp):
TATATACATAGTTTA
Found at i:362933 original size:19 final size:20
Alignment explanation
Indices: 362879--362934 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
362869 ATAGTTTTTA
* *
362879 TATATAGTTTATACATAAACT
1 TATATATTTTA-ATATAAACT
*
362900 TATATTATATTAATATAAA-T
1 TATA-TATTTTAATATAAACT
362920 TATATATTTTAATAT
1 TATATATTTTAATAT
362935 TATATAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 10 0.33
22 5 0.17
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATTTTAATATAAACT
Found at i:362936 original size:15 final size:16
Alignment explanation
Indices: 362913--362951 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
362903 ATTATATTAA
* *
362913 TATAAATTATATATTT
1 TATATATTATATAGTT
362929 TA-ATATTATATAGTT
1 TATATATTATATAGTT
362944 TATATATT
1 TATATATT
362952 GTTACACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TATATATTATATAGTT
Found at i:363055 original size:2 final size:2
Alignment explanation
Indices: 363050--363193 Score: 66
Period size: 2 Copynumber: 72.5 Consensus size: 2
363040 CTTAATATGC
* * * *
363050 TA TA TA TA TA AA CTA TA TA CA TA AA TC T- TA TA TA T- TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
363091 TT TA TA TA TA TA TA TA T- TA CA TA GTT TA T- TA -A TA AA CTA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * * * *
363132 TA TA AA CTA TA TA TA T- TA TA TA TT TG TC TT TA TA TA CTT TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
363175 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
363194 TTTTTTCAAT
Statistics
Matches: 105, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
1 6 0.06
2 94 0.90
3 5 0.05
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:363065 original size:13 final size:14
Alignment explanation
Indices: 363049--363102 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
363039 ACTTAATATG
363049 CTATATATATAAA-
1 CTATATATATAAAT
*
363062 CTATATACATAAAT
1 CTATATATATAAAT
*
363076 CTTATATATTATATAT
1 C-TATATA-TATAAAT
*
363092 TTATATATATA
1 CTATATATATA
363103 TATATTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.35
14 5 0.15
15 12 0.35
16 5 0.15
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (14 bp):
CTATATATATAAAT
Found at i:368910 original size:21 final size:21
Alignment explanation
Indices: 368876--368947 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 21
368866 AAGGTGAAAT
* *
368876 TATTATAATATTTTAAAATTAA
1 TATT-TAATTTTTTAAAATAAA
*
368898 TATTTAATTTTTTATAATAAA
1 TATTTAATTTTTTAAAATAAA
*
368919 TAATATTAATTATTATATTAAATAAA
1 T-AT-TTAATT-TT-T-TAAAATAAA
368945 TAT
1 TAT
368948 CATAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
21 15 0.38
22 6 0.15
23 6 0.15
24 2 0.05
25 3 0.08
26 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTAATTTTTTAAAATAAA
Found at i:368940 original size:22 final size:24
Alignment explanation
Indices: 368895--368943 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
368885 ATTTTAAAAT
*
368895 TAATATTTAATTTTTTATAATAAA
1 TAATATTTAATTTATTATAATAAA
*
368919 TAATA-TTAA-TTATTATATTAAA
1 TAATATTTAATTTATTATAATAAA
368941 TAA
1 TAA
368944 ATATCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 4 0.17
24 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATATTTAATTTATTATAATAAA
Found at i:372369 original size:138 final size:135
Alignment explanation
Indices: 372163--372534 Score: 549
Period size: 139 Copynumber: 2.7 Consensus size: 135
372153 TATAAGTACC
* **
372163 CAAAGTGGTGAAAGCGCGTTCCCAGGGGGCGCCTTTGATTATTTTGTC------ATGTTATCATT
1 CAAAGTGGTGAAAGCGCGTT-CCGGGGGGCGCCTTCCATTATTTTGTCAGAAATATGTTATCATT
*
372222 GCCCTATTATGTCACTCATGTCCCCCGGATAACTATTCATGTCAGTACCTATTATTTCTGAGGGG
65 GCCCTATTATGTCACTCATGTCCCCCGGAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGG
372287 ACTTGG
130 ACTTGG
*
372293 CTAAGTGGTGAAAGCGCGTTCTCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTC-CGGGGG-GCGCCTTCCATTATTTTGTCAGA-AATATGTTATCA
* *
372358 TTGCCCTATTATGTCACTCATGTCCCCCCGGAGAACTAATCATGTCAGTACTTATTATTTCTGAG
63 TTGCCCTATTATGTCACTCATGT-CCCCCGGAGAACTATTCATGTCAGTACCTATTATTTCTGAG
372423 GGGACTTGG
127 GGGACTTGG
* *
372432 CAAAGTGGTGAAAGCGCGTTCCTGGGGGCGTGTCTTCCATTATTTTGTCAGATAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCC-GGGGG-GCGCCTTCCATTATTTTGTCAGA-AATATGTTATCA
372497 TTGCCCTATTATGTCACTCATGTCCCCCGGAGAACTAT
63 TTGCCCTATTATGTCACTCATGTCCCCCGGAGAACTAT
372535 AGATGGATGG
Statistics
Matches: 218, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
129 1 0.00
130 24 0.11
131 18 0.08
138 47 0.22
139 128 0.59
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (135 bp):
CAAAGTGGTGAAAGCGCGTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCCCGGAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGA
CTTGG
Found at i:372693 original size:23 final size:22
Alignment explanation
Indices: 372667--372709 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
372657 ATGTGAAGTT
*
372667 TGAATAAATTGTATGAAATGTTA
1 TGAATAAATTGAAT-AAATGTTA
372690 TGAATAAATTGAATAAATGT
1 TGAATAAATTGAATAAATGT
372710 GAAGTGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (22 bp):
TGAATAAATTGAATAAATGTTA
Found at i:372732 original size:63 final size:63
Alignment explanation
Indices: 372664--372791 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 63
372654 GTTATGTGAA
* *
372664 GTTTGAATAAATT-GTATGAAATGTTATGAATAAATTGAATAAATGTGAAGTGATCAA-TTGGTT
1 GTTTGAATAAATTAG-ATAAAATGTTATGAACAAATTGAATAAATGTGAAGTGAT-AAGTTGGTT
* *
372727 GTTTGAATATATTAGATAAAATGTTATGGACAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATGAACAAATTGAATAAATGTGAAGTGATAAGTTGGTT
372790 GT
1 GT
372792 GACATTGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
62 2 0.03
63 56 0.95
64 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTAGATAAAATGTTATGAACAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:372876 original size:14 final size:14
Alignment explanation
Indices: 372857--372901 Score: 90
Period size: 14 Copynumber: 3.2 Consensus size: 14
372847 TGATAAGTTG
372857 GTTTTAATGTATAT
1 GTTTTAATGTATAT
372871 GTTTTAATGTATAT
1 GTTTTAATGTATAT
372885 GTTTTAATGTATAT
1 GTTTTAATGTATAT
372899 GTT
1 GTT
372902 AAGGATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:373641 original size:21 final size:21
Alignment explanation
Indices: 373590--373641 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
373580 GGTATCATAA
*
373590 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
373611 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
373632 AACCCTGCGG
1 AACCCTGCGG
373642 AGATGACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:373665 original size:42 final size:42
Alignment explanation
Indices: 373614--373707 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
373604 GGCATGTAAC
* * *
373614 CTGGCGGGCTAGGAATGTAACCCTGCGGAGATGACATATAAA
1 CTGGAGGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
* * * * * *
373656 CTGGTGGGCTTGGCATATACCCCTGAGGAGATGACATCTGAA
1 CTGGAGGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
373698 CTGGAGGGCT
1 CTGGAGGGCT
373708 GGGCATCATC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (42 bp):
CTGGAGGGCTAGGAATATAACCCTGAGGAGATGACATATAAA
Found at i:373713 original size:42 final size:42
Alignment explanation
Indices: 373634--373713 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
373624 AGGAATGTAA
* * *
373634 CCCTGCGGAGATGACATATAAACTGGTGGGCTTGGCATATAC
1 CCCTGAGGAGATGACATATAAACTGGAGGGCTGGGCATATAC
* *
373676 CCCTGAGGAGATGACATCTGAACTGGAGGGCTGGGCAT
1 CCCTGAGGAGATGACATATAAACTGGAGGGCTGGGCAT
373714 CATCATCGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (42 bp):
CCCTGAGGAGATGACATATAAACTGGAGGGCTGGGCATATAC
Found at i:375369 original size:18 final size:18
Alignment explanation
Indices: 375315--375405 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
375305 ACTAAATATT
375315 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
375334 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* *
375353 TGTCCCAAAGGACCACTC
1 TGTCCCGAAGGACCACTA
*
375371 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
375389 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
375406 GATAATCCCT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
18 44 0.73
19 1 0.02
20 15 0.25
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:377409 original size:18 final size:17
Alignment explanation
Indices: 377376--377409 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
377366 GAATAATTAA
377376 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
377393 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
377410 AAACATACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:385470 original size:18 final size:20
Alignment explanation
Indices: 385415--385473 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
385405 CACTGAATAT
* *
385415 TTGTCTCGAAGGGCCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
385435 TTGTTCCGAAGAATCACT-A
1 TTGTCCCGAAGGACCACTGA
385454 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
385473 T
1 T
385474 AATCCCTCGA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 14 0.48
19 2 0.07
20 13 0.45
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:385731 original size:2 final size:2
Alignment explanation
Indices: 385724--385751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
385714 TAATACATAC
385724 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
385752 GTATGCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:387692 original size:30 final size:30
Alignment explanation
Indices: 387611--387706 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
387601 TAATTATCAC
* *
387611 AAAAAATAATTAATTA-ATAA--ATTTAAAT
1 AAAAAATAA-TATTTATATAATTATTTTAAT
* * *
387639 AAATAATAAT-TATATAAATATTATTTTAAT
1 AAAAAATAATATTTATATA-ATTATTTTAAT
* *
387669 AAAAAATAATATTTATATAATTATATTACT
1 AAAAAATAATATTTATATAATTATTTTAAT
*
387699 ATAAAATA
1 AAAAAATA
387707 TAAAAACGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 9 0.17
30 32 0.62
31 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATATTTATATAATTATTTTAAT
Found at i:388345 original size:3 final size:3
Alignment explanation
Indices: 388337--388400 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
388327 CCATGAACAC
388337 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
388385 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
388401 CCTTCTAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:390680 original size:25 final size:25
Alignment explanation
Indices: 390635--390683 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
390625 GTACAAAGGC
*
390635 AAGAAATTAACATACTGTATTGTTA
1 AAGAAATTAACATACTATATTGTTA
*
390660 AAGAGATTAACA-AGCTATATTGTT
1 AAGAAATTAACATA-CTATATTGTT
390684 TCTCATGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (25 bp):
AAGAAATTAACATACTATATTGTTA
Found at i:405545 original size:28 final size:27
Alignment explanation
Indices: 405513--405593 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
405503 TTCTATTTGA
405513 ATTTAATGTTAAATAAAAAAATAATTAT
1 ATTTAAT-TTAAATAAAAAAATAATTAT
* * * *
405541 ATTTAATATTATATAATAAAATTATTGT
1 ATTTAAT-TTAAATAAAAAAATAATTAT
405569 A-TTAACTTTAATATAAAACAAATAA
1 ATTTAA-TTTAA-ATAAAA-AAATAA
405594 ATTTAAGTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 7 0.17
28 30 0.71
29 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAATTTAAATAAAAAAATAATTAT
Found at i:409115 original size:14 final size:14
Alignment explanation
Indices: 409096--409127 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
409086 TGTTTAATAT
409096 TTAAAAAATTAATG
1 TTAAAAAATTAATG
409110 TTAAAAAATTAATG
1 TTAAAAAATTAATG
409124 TTAA
1 TTAA
409128 TATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
TTAAAAAATTAATG
Found at i:411839 original size:17 final size:17
Alignment explanation
Indices: 411817--411849 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
411807 ATATGAACAC
411817 CAATAA-ATAATAAAAAT
1 CAATAATAT-ATAAAAAT
411834 CAATAATATATAAAAA
1 CAATAATATATAAAAA
411850 ATTATCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
CAATAATATATAAAAAT
Found at i:420918 original size:20 final size:21
Alignment explanation
Indices: 420893--420985 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
420883 TTTTCCCAAT
420893 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* * ** *
420913 TCGCAAAGCAAATTGGGGAAA
1 TCGCAATGCGAATTAAGTAAA
420934 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* ** *
420954 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGTAAA
420975 TCGCAATGCGA
1 TCGCAATGCGA
420986 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGTAAA
Done.