Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001650.1 Hibiscus syriacus cultivar Beakdansim tig00003301_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: 96756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1248 original size:95 final size:95
Alignment explanation
Indices: 1101--1303 Score: 282
Period size: 95 Copynumber: 2.1 Consensus size: 95
1091 TACCAATGAG
* * * *
1101 GTAGTATCAATACCATGGTAAGGGTATTGATACCAAGCAACATAGAATCTAAATTTGGTATCGAT
1 GTAGTATCAATACCACGGTAAGGGTATCGATACCAAGAAACATAGAACCTAAATTTGGTATCGAT
1166 ACCGAAAGGGGGTATCGATACCATAGTATT
66 ACCGAAAGGGGGTATCGATACCATAGTATT
* *
1196 GTAGTATGAATACCACGGTAAGGGTATCGATACCAGGAAACATCA-AACCTAAATTTGGTATCGA
1 GTAGTATCAATACCACGGTAAGGGTATCGATACCAAGAAACAT-AGAACCTAAATTTGGTATCGA
* * * *
1260 TACTGGAATGGGGTATCGCTACCATAGTATT
65 TACCGAAAGGGGGTATCGATACCATAGTATT
* *
1291 GAAGTATCGATAC
1 GTAGTATCAATAC
1304 TCGGGTAGTA
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 93 0.99
96 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (95 bp):
GTAGTATCAATACCACGGTAAGGGTATCGATACCAAGAAACATAGAACCTAAATTTGGTATCGAT
ACCGAAAGGGGGTATCGATACCATAGTATT
Found at i:1709 original size:55 final size:53
Alignment explanation
Indices: 1634--1919 Score: 282
Period size: 55 Copynumber: 5.4 Consensus size: 53
1624 GATTACCATG
*** *
1634 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATGACCGT
1 TCGGCACTAAGTGTGCATTTCAAAAAATTCATCCTATGTGGATGAATAACCGT
* * *
1687 TCGACACTAAGTGTGTGCATTTCAAAAAATTCATCATATAG-GGATGAATGACCGTT
1 TCGGCACTAA--GTGTGCATTTCAAAAAATTCATCCTAT-GTGGATGAATAACCG-T
* ***
1743 TCGGCTCTAA--GTGCATTTCATGGAATTCATCCTA--TGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCAAAAAATTCATCCTATGTGGATGAATAACCG-T
* * * **
1793 TCGGCACTAAGTGTGCATTTCACAAAATTCATCCTGTATGGATGAATAACTATT
1 TCGGCACTAAGTGTGCATTTCAAAAAATTCATCCTATGTGGATGAATAAC-CGT
* *
1847 TCGACACTAAGTGTGCATTTCAAAAAAATTCATCTTATGTGGATGAATAACC-T
1 TCGGCACTAAGTGTGCATTTC-AAAAAATTCATCCTATGTGGATGAATAACCGT
*
1900 TTGGCACTAA--GTGCATTTCA
1 TCGGCACTAAGTGTGCATTTCA
1920 CGGGATTCAT
Statistics
Matches: 195, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
50 24 0.12
51 9 0.05
52 40 0.21
53 18 0.09
54 33 0.17
55 61 0.31
56 10 0.05
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (53 bp):
TCGGCACTAAGTGTGCATTTCAAAAAATTCATCCTATGTGGATGAATAACCGT
Found at i:1770 original size:107 final size:108
Alignment explanation
Indices: 1628--1912 Score: 321
Period size: 104 Copynumber: 2.7 Consensus size: 108
1618 TGTGGTGATT
* * * * *
1628 ACCATGTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATGACCGTTCGACA
1 ACCATTTCGACACTAAG-GTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTCGGCA
*
1693 CTAAGTGTGTGCATTTCAAAAAATTCATCATATAGGGATGAATG
65 CTAAGTGTGTGCATTTCAAAAAATTCATCATATAGGGATGAATA
* * * *
1737 ACCGTTTCGGCTCTAA-GTGCATTTCATGGAATTCATCCTA--TGGATGAATAACCGTTTCGGCA
1 ACCATTTCGACACTAAGGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCG-TTCGGCA
* * * *
1799 CTAA--GTGTGCATTTCACAAAATTCATCCTGTATGGATGAATA
65 CTAAGTGTGTGCATTTCAAAAAATTCATCATATAGGGATGAATA
* ** * *
1841 ACTATTTCGACACTAAGTGTGCATTTCAAAAAAATTCATCTTATGTGGATGAATAACC-TTTGGC
1 ACCATTTCGACACTAAG-GTGCATTTC-AAGGAATTCATCCTATGTGGATGAATAACCGTTCGGC
1905 ACTAAGTG
64 ACTAAGTG
1913 CATTTCACGG
Statistics
Matches: 148, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
104 45 0.30
105 13 0.09
106 19 0.13
107 44 0.30
109 27 0.18
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (108 bp):
ACCATTTCGACACTAAGGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTCGGCAC
TAAGTGTGTGCATTTCAAAAAATTCATCATATAGGGATGAATA
Found at i:7896 original size:93 final size:95
Alignment explanation
Indices: 7794--7979 Score: 261
Period size: 93 Copynumber: 2.0 Consensus size: 95
7784 ACCAATGAGG
* * *
7794 TAGTATCGATACCATAGTAAGGG-TAGCGATACCAAGCAACAT-GAATCTAAATTTGGTATCGAT
1 TAGTATCGATACCATAGT-AGGGTTAGCGATACCAAGAAACATCGAACCTAAATTTGGCATCGAT
*
7857 ACCAGAAGGGGGTA-CGGTACCATAGTATTA
65 ACCAGAAGGGGGTATCAGTACCATAGTATTA
* *
7887 TAGTATCGATACCATGGTAGGGTTATCGATACCAAGAAACATCGAACCTAAATTTGGCATCGATA
1 TAGTATCGATACCATAGTAGGGTTAGCGATACCAAGAAACATCGAACCTAAATTTGGCATCGATA
* * *
7952 TCGGAATGGGGTATCAGTACCATAGTAT
66 CCAGAAGGGGGTATCAGTACCATAGTAT
7980 AGAAGTATCG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
92 4 0.05
93 34 0.42
94 30 0.37
95 13 0.16
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (95 bp):
TAGTATCGATACCATAGTAGGGTTAGCGATACCAAGAAACATCGAACCTAAATTTGGCATCGATA
CCAGAAGGGGGTATCAGTACCATAGTATTA
Found at i:8001 original size:95 final size:93
Alignment explanation
Indices: 7795--8001 Score: 238
Period size: 93 Copynumber: 2.2 Consensus size: 93
7785 CCAATGAGGT
** * * * *
7795 AGTATCGATACCATAGTAAGGG-TAGCGATACCAAGCAACATGAATCTAAATTTGGTATCGATAC
1 AGTATCGATACCAGGGT-AGGGTTATCGATACCAAGAAACATGAACCTAAATTTGGCATCGATAC
* *
7859 CAGAAGGGGGTACGGTACCATAGTATTAT
65 CAGAAGGGGGTACAGTACCATAGTATTAA
* *
7888 AGTATCGATACCATGGTAGGGTTATCGATACCAAGAAACATCGAACCTAAATTTGGCATCGATAT
1 AGTATCGATACCAGGGTAGGGTTATCGATACCAAGAAACAT-GAACCTAAATTTGGCATCGATAC
* *
7953 CGGAATGGGGTATCAGTACCATAGTA-TAGA
65 CAGAAGGGGGTA-CAGTACCATAGTATTA-A
* *
7983 AGTATCGGTACTAGGGTAG
1 AGTATCGATACCAGGGTAG
8002 TAGTATCGAT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
92 4 0.04
93 33 0.34
94 32 0.33
95 28 0.29
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (93 bp):
AGTATCGATACCAGGGTAGGGTTATCGATACCAAGAAACATGAACCTAAATTTGGCATCGATACC
AGAAGGGGGTACAGTACCATAGTATTAA
Found at i:8009 original size:95 final size:93
Alignment explanation
Indices: 7820--8013 Score: 230
Period size: 95 Copynumber: 2.1 Consensus size: 93
7810 GTAAGGGTAG
* * * *
7820 CGATACCAAGCAACATGAATCTAAATTTGGTATCGATACCAGAAGGGGGTACGGTACCATAGTAT
1 CGATACCAAGAAACATGAACCTAAATTTGGCATCGATACCAGAAGGGGGTACAGTACCATAGTAT
* * *
7885 TATAGTATCGATACCATGGTAGGGTTAT
66 TAAAGTATCGATACCAGGGTAGAGTTAT
* * *
7913 CGATACCAAGAAACATCGAACCTAAATTTGGCATCGATATCGGAATGGGGTATCAGTACCATAGT
1 CGATACCAAGAAACAT-GAACCTAAATTTGGCATCGATACCAGAAGGGGGTA-CAGTACCATAGT
* *
7978 A-TAGAAGTATCGGTACTAGGGTAGTAG-TAT
64 ATTA-AAGTATCGATACCAGGGTAG-AGTTAT
8008 CGATAC
1 CGATAC
8014 TATGGAGCCA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
93 15 0.18
94 32 0.38
95 37 0.44
96 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (93 bp):
CGATACCAAGAAACATGAACCTAAATTTGGCATCGATACCAGAAGGGGGTACAGTACCATAGTAT
TAAAGTATCGATACCAGGGTAGAGTTAT
Found at i:8749 original size:54 final size:54
Alignment explanation
Indices: 8336--8742 Score: 508
Period size: 54 Copynumber: 7.5 Consensus size: 54
8326 TACCAAGTCA
* *
8336 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATGACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* * * * *
8390 GCACTAAGTGTGCATTTCACGAAATTCATCATATGGGGATGAATGACCATTTCT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
*
8444 GCTCTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* * * * * **
8498 GCACTAAATGTTCATTTCATGAAATTCATCTTATGTGGATGAATAACTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* * ** * * **
8552 ACACTAAGTGTGAATTTCACATAATTTATCCTATGTGGATAAATAACTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* * * * *
8606 ACACTAAGTTTACATTCCACGGAATTCATTCTATGTGGATGAATAACCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* * * *
8660 ACACTAAATGTGCATTTCACGGAATTCGTCCTATGTGGATAAATAACCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
* *
8714 GCACTAAGTGTGCATTTCTCGGGATTCAT
1 GCACTAAGTGTGCATTTCACGGAATTCAT
8743 AATATGTTAT
Statistics
Matches: 301, Mismatches: 52, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 301 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCG
Found at i:10840 original size:16 final size:15
Alignment explanation
Indices: 10805--10841 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
10795 CACATATATT
*
10805 GAAAACATAAAGTAA
1 GAAAAAATAAAGTAA
*
10820 GAAAAAATAATGTAA
1 GAAAAAATAAAGTAA
10835 GAAAAAA
1 GAAAAAA
10842 GGTCTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
GAAAAAATAAAGTAA
Found at i:12179 original size:16 final size:17
Alignment explanation
Indices: 12150--12183 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12140 CAAATTACAC
12150 AAAAACAGAAAATAAAT
1 AAAAACAGAAAATAAAT
*
12167 AAAAA-AGATAATAAAT
1 AAAAACAGAAAATAAAT
12183 A
1 A
12184 GTAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAACAGAAAATAAAT
Found at i:12190 original size:7 final size:7
Alignment explanation
Indices: 12160--12206 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
12150 AAAAACAGAA
12160 AATAAAT
1 AATAAAT
*
12167 AAAAAAGAT
1 -AATAA-AT
12176 AATAAAT
1 AATAAAT
*
12183 AGTAAAT
1 AATAAAT
12190 AATAAAT
1 AATAAAT
12197 AATAAAT
1 AATAAAT
12204 AAT
1 AAT
12207 CCAATATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
7 24 0.71
8 8 0.24
9 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:12271 original size:20 final size:22
Alignment explanation
Indices: 12231--12279 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
12221 TACTATAAGA
12231 AATATTATTTTCAAGAAACTAT
1 AATATTATTTTCAAGAAACTAT
12253 AATA-TATTTTCAA-AAACTAT
1 AATATTATTTTCAAGAAACTAT
12273 -ATATTAT
1 AATATTAT
12280 ATATAGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.12
20 10 0.38
21 9 0.35
22 4 0.15
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATTATTTTCAAGAAACTAT
Found at i:12281 original size:22 final size:21
Alignment explanation
Indices: 12231--12273 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
12221 TACTATAAGA
12231 AATATTATTTTCAAGAAACTAT
1 AATA-TATTTTCAAGAAACTAT
12253 AATATATTTTCAA-AAACTAT
1 AATATATTTTCAAGAAACTAT
12273 A
1 A
12274 TATTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (21 bp):
AATATATTTTCAAGAAACTAT
Found at i:12291 original size:28 final size:30
Alignment explanation
Indices: 12259--12314 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
12249 CTATAATATA
12259 TTTTCAAAA-ACTATATAT-TATATATAGG
1 TTTTCAAAATACTATATATATATATATAGG
* *
12287 TTTTCAAAATATTTTATATATATATATA
1 TTTTCAAAATACTATATATATATATATA
12315 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 7 0.29
30 8 0.33
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (30 bp):
TTTTCAAAATACTATATATATATATATAGG
Found at i:12308 original size:2 final size:2
Alignment explanation
Indices: 12301--12343 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12291 CAAAATATTT
12301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12343 T
1 T
12344 TCAAAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12367 original size:38 final size:38
Alignment explanation
Indices: 12325--12637 Score: 349
Period size: 37 Copynumber: 8.4 Consensus size: 38
12315 TATATATATA
* *
12325 TATATATATATATATATATTCAAAATGTTTTCAAAAAC
1 TATATATATATATATATTTTCAAAATATTTTCAAAAAC
* *
12363 TATAT-TATATATATATATTCAAAATGTTTTCAAAAAC
1 TATATATATATATATATTTTCAAAATATTTTCAAAAAC
* *
12400 --TATATATATATAT-TTTTCAAAATACTTTCGAAAAC
1 TATATATATATATATATTTTCAAAATATTTTCAAAAAC
*
12435 TATATAT-TATATATATTTTCAAAATATTTTCAAGAAC
1 TATATATATATATATATTTTCAAAATATTTTCAAAAAC
**
12472 TATATAT-TATATATATGTTTCAAAATATTTTTTAAAAC
1 TATATATATATATATAT-TTTCAAAATATTTTCAAAAAC
* *
12510 TATATAT-TATATATTGTTTTCAAAATATTTTCAAAAAA
1 TATATATATATATA-TATTTTCAAAATATTTTCAAAAAC
* *
12548 TATATATTATACATATGTTTTCAAAATATTTTC-AAAAC
1 TATATA-TATATATATATTTTCAAAATATTTTCAAAAAC
* **** *
12586 TATATATCATATGT-TATCGAAAAAATATTTTCCAAAAC
1 TATATAT-ATATATATATTTTCAAAATATTTTCAAAAAC
12624 TATATAT-TATATAT
1 TATATATATATATAT
12638 TATATATATA
Statistics
Matches: 240, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
35 21 0.09
36 20 0.08
37 87 0.36
38 86 0.36
39 21 0.09
40 5 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATATATATATATTTTCAAAATATTTTCAAAAAC
Found at i:12379 original size:37 final size:36
Alignment explanation
Indices: 12327--12638 Score: 344
Period size: 38 Copynumber: 8.4 Consensus size: 36
12317 TATATATATA
* *
12327 TATATATATATATATATTCAAAATGTTTTCAAAAAC
1 TATATATATATATATTTTCAAAATATTTTCAAAAAC
* *
12363 TATATTATATATATATATTCAAAATGTTTTCAAAAAC
1 TATA-TATATATATATTTTCAAAATATTTTCAAAAAC
* *
12400 TATATATATATAT-TTTTCAAAATACTTTCGAAAAC
1 TATATATATATATATTTTCAAAATATTTTCAAAAAC
*
12435 TATATATTATATATATTTTCAAAATATTTTCAAGAAC
1 TATATA-TATATATATTTTCAAAATATTTTCAAAAAC
**
12472 TATATATTATATATATGTTTCAAAATATTTTTTAAAAC
1 TATATA-TATATATAT-TTTCAAAATATTTTCAAAAAC
* *
12510 TATATATTATATATTGTTTTCAAAATATTTTCAAAAAA
1 TATATA-TATATA-TATTTTCAAAATATTTTCAAAAAC
*
12548 TATATATTATACATATGTTTTCAAAATATTTTC-AAAAC
1 TATATA-TAT--ATATATTTTCAAAATATTTTCAAAAAC
* * * *
12586 TATATAT-CATATGTTATCGAAAAAATATTTTCCAAAAC
1 TATATATATATATATTTTC---AAAATATTTTCAAAAAC
12624 TATATAT-TATATATT
1 TATATATATATATATT
12639 ATATATATAC
Statistics
Matches: 246, Mismatches: 19, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
34 9 0.04
35 24 0.10
36 20 0.08
37 83 0.34
38 87 0.35
39 20 0.08
40 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATATATATATTTTCAAAATATTTTCAAAAAC
Found at i:21119 original size:13 final size:14
Alignment explanation
Indices: 21101--21129 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21091 CTCACCTGGC
21101 ATGCCTTACT-ATT
1 ATGCCTTACTCATT
21114 ATGCCTTACTCATT
1 ATGCCTTACTCATT
21128 AT
1 AT
21130 CCGATTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (14 bp):
ATGCCTTACTCATT
Found at i:22190 original size:21 final size:22
Alignment explanation
Indices: 22165--22210 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
22155 AAATAAATGG
22165 TTTCATG-AAATTTATCCTTA-A
1 TTTCATGTAAATTTA-CCTTATA
*
22186 TTTCATGTTAATTTACCTTATA
1 TTTCATGTAAATTTACCTTATA
22208 TTT
1 TTT
22211 AAGCTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCATGTAAATTTACCTTATA
Found at i:29337 original size:14 final size:14
Alignment explanation
Indices: 29318--29347 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29308 TGCAAGGAGC
29318 CGGGATATATGAAG
1 CGGGATATATGAAG
29332 CGGGATATATGAAG
1 CGGGATATATGAAG
29346 CG
1 CG
29348 AGACTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (14 bp):
CGGGATATATGAAG
Found at i:57519 original size:56 final size:58
Alignment explanation
Indices: 57420--57587 Score: 216
Period size: 56 Copynumber: 2.9 Consensus size: 58
57410 ATTGAGGATA
* * * * *
57420 GCACTAAAGTATAACTAGTGCATATGGTGGGTACGGCCATATGTGTCATACT-TGGGATT
1 GCACTAAAGTAT-A-TAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCCGGGACT
*
57479 TCACTAAAGTAT-TAGTGCATATGGTGGGCACGACCTTATGTGTCATA-TCCGGGACT
1 GCACTAAAGTATATAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCCGGGACT
*
57535 GCACTAAAGTATAACTAGTGCATATGGTGAGCACGACCTTATGTGTCATACTC
1 GCACTAAAGTAT-A-TAGTGCATATGGTGGGCACGACCTTATGTGTCATACTC
57588 GGGTTAGCAC
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
55 1 0.01
56 48 0.50
59 45 0.47
60 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (58 bp):
GCACTAAAGTATATAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCCGGGACT
Found at i:57598 original size:59 final size:59
Alignment explanation
Indices: 57415--57599 Score: 245
Period size: 59 Copynumber: 3.2 Consensus size: 59
57405 TGTATATTGA
* * * * *
57415 GGATAGCACTAAAGTATAACTAGTGCATATGGTGGGTACGGCCATATGTGTCATACTTG
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCG
*
57474 GGATTTCACTAAAGTAT---TAGTGCATATGGTGGGCACGACCTTATGTGTCATA-TCCG
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACT-CG
* *
57530 GGACTGCACTAAAGTATAACTAGTGCATATGGTGAGCACGACCTTATGTGTCATACTCG
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCG
57589 GG-TTAGCACTA
1 GGATT-GCACTA
57600 CGGTGAATAT
Statistics
Matches: 110, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
55 1 0.01
56 48 0.44
58 1 0.01
59 59 0.54
60 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (59 bp):
GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCG
Found at i:57991 original size:36 final size:36
Alignment explanation
Indices: 57951--58022 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
57941 CTTGGCATCA
*
57951 ATCACAATGGAAGTATTTACAAGTCACAATGATGAC
1 ATCACAAAGGAAGTATTTACAAGTCACAATGATGAC
57987 ATCACAAAGGAAGTATTTACAAGTCACAATGATGAC
1 ATCACAAAGGAAGTATTTACAAGTCACAATGATGAC
58023 TTCTTACTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (36 bp):
ATCACAAAGGAAGTATTTACAAGTCACAATGATGAC
Found at i:60232 original size:20 final size:20
Alignment explanation
Indices: 60207--60247 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
60197 GTTGACCTAT
*
60207 CTGTTGACCGTTGACTTTGA
1 CTGTTGACCATTGACTTTGA
*
60227 CTGTTGTCCATTGACTTTGA
1 CTGTTGACCATTGACTTTGA
60247 C
1 C
60248 CACAAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
CTGTTGACCATTGACTTTGA
Found at i:68795 original size:16 final size:16
Alignment explanation
Indices: 68774--68815 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
68764 AGAACCATTT
68774 CGCCACCCTTGAACAA
1 CGCCACCCTTGAACAA
*
68790 CGCCACCCTTGAACGA
1 CGCCACCCTTGAACAA
*
68806 CGCCGCCCTT
1 CGCCACCCTT
68816 CTCTCCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.48, G:0.17, T:0.14
Consensus pattern (16 bp):
CGCCACCCTTGAACAA
Found at i:69797 original size:22 final size:22
Alignment explanation
Indices: 69770--69821 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
69760 TTTAATAAAA
69770 TATTAATAAAATAAATTTGAGT
1 TATTAATAAAATAAATTTGAGT
69792 TATTAATAAAATAAATTTGAGT
1 TATTAATAAAATAAATTTGAGT
69814 TATTAATA
1 TATTAATA
69822 GATGACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (22 bp):
TATTAATAAAATAAATTTGAGT
Found at i:71897 original size:11 final size:11
Alignment explanation
Indices: 71881--71907 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
71871 ATATGACTAA
71881 AATAAAATAAT
1 AATAAAATAAT
71892 AATAAAATAAT
1 AATAAAATAAT
71903 AATAA
1 AATAA
71908 TTAAAGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:73788 original size:123 final size:121
Alignment explanation
Indices: 73569--74543 Score: 838
Period size: 113 Copynumber: 8.3 Consensus size: 121
73559 GAACAAATTC
* * * * * *
73569 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTAATACTGATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAT--TGATGCTGATCTAT
* * * *
73634 CTCATTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
64 CTCCTTCTG-GATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
73692 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAATTGATGCTGATCTATC
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG-AAAATTGATGCTGATCTATC
* * *
73757 TCCTTCTGCGATAGAGTCGAGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
65 TCCTTCTG-GATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* *
73815 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATTTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-GAAA-ATTGATGCTGATCTAT
* * * *
73879 ATCCTTCTGGGATAGAGTCGAGCAAAAGGTTTAACAAGTTCTTCTTATTATGAACTTCT
64 CTCCTTCT-GGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * ** *
73938 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAA-TG-T--TGATCCA--
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGAAAATTGATGCTGATCTATC
*** *
73996 T-CGAAT-GAT-GAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 TCCTTCTGGATAG-AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * * * *
74051 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGGCTCTGCTGCTATAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAATTG--ATGCTGATCTAT
* * * *
74116 CTCTTTCTGAAATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTAT
64 CTCCTTCTG-GATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * * *
74175 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACT-TGACAA-TG-T--TAATCCA--
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGAAAATTGATGCTGATCTATC
*** * *
74233 T-CGAAT-GAT-GAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 TCCTTCTGGATAG-AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
** *
74288 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-C-GGCAA-TG-T--TGATCCA--
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGAAAATTGATGCTGATCTATC
*** * * * *
74344 T-CGAGT-GATAAATTCAAGCAAAAAGTTGAACAAGTTC-T-T-ATTATTAACTTCT
65 TCCTTCTGGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* ** ** *
74396 TC-TCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAC-CTG-GCA---ATGCTGATCCA--
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGAAAATTGATGCTGATCTATC
*** * *
74453 T-CGAGT-GAT-GAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 TCCTTCTGGATAG-AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* *
74508 TCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAAC
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
74544 CCTTCTGGAA
Statistics
Matches: 734, Mismatches: 83, Indels: 80
0.82 0.09 0.09
Matches are distributed among these distances:
107 4 0.01
108 47 0.06
109 42 0.06
110 2 0.00
111 48 0.07
112 51 0.07
113 163 0.22
114 1 0.00
115 3 0.00
116 2 0.00
117 1 0.00
118 8 0.01
119 4 0.01
120 2 0.00
121 3 0.00
122 69 0.09
123 157 0.21
124 121 0.16
125 6 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (121 bp):
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAATTGATGCTGATCTATCT
CCTTCTGGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
Found at i:74028 original size:113 final size:113
Alignment explanation
Indices: 73899--74543 Score: 863
Period size: 113 Copynumber: 5.7 Consensus size: 113
73889 GATAGAGTCG
* * *
73899 AGCAAAAGGTTTAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
73964 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
66 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
74012 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *** **
74077 CATTATGAACT-TTCTCTGGAAATGGCTCTGCTGCTATATCTCTTTCTGAAATAGAGTCA
66 CATTATGAACTCTAC-CTGGCAAT-G-T-TGAT-C--CATCGAATGATG-AAT----TCA
* *
74136 AACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
74201 CATTATGAACTCTACTTGACAATGTTAATCCATCGAATGATGAATTCA
66 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
*
74249 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
74313 CATTATGAACTCTTCC-GGCAATGTTGATCCATCGAGTGATAAATTCA
66 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
* *
74360 AGCAAAAAGTTGAACAAGTTC-T-T-ATTATTAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
74421 TATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTCG
66 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
* *
74469 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
74534 CATTATGAAC
66 CATTATGAAC
74544 CCTTCTGGAA
Statistics
Matches: 466, Mismatches: 47, Indels: 38
0.85 0.09 0.07
Matches are distributed among these distances:
107 3 0.01
108 46 0.10
109 49 0.11
110 2 0.00
111 49 0.11
112 49 0.11
113 155 0.33
114 1 0.00
115 1 0.00
116 3 0.01
117 4 0.01
118 6 0.01
119 6 0.01
120 4 0.01
121 2 0.00
122 1 0.00
123 1 0.00
124 82 0.18
125 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
Found at i:74154 original size:237 final size:234
Alignment explanation
Indices: 73569--74556 Score: 1140
Period size: 237 Copynumber: 4.2 Consensus size: 234
73559 GAACAAATTC
* * * *
73569 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTAATACTGATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATGCTGAT-TAT
* *
73634 CTCATTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
65 CTC-TTCTG-GATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * * **
73698 TTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGAAAAATTGATGCTGATCTATCTCCTT
128 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTG-ACAA-TG-T--TGATCCA--T-CGA
* * * * *
73762 CTGCGAT-AGAGTCGAGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
184 AT--GATGA-ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* *
73815 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATTTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATGCTGA-TTAT
* * * * * *
73879 ATCCTTCTGGGATAGAGTCGAGCAAAAGGTTTAACAAGTTCTTCTTATTATGAACTTCTTCTTCT
65 CT-CTTCT-GGATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
*
73944 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAAT
128 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGACAATGTTGATCCATCGAATGATGAAT
74009 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
193 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* *
74051 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGGCT-CTGCTGCTATA
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAT-GCTAATGCTGAT-TA
* *
74115 TCTCTTTCTGAAATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTC
64 TCTC-TTCTG-GATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
* *
74180 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTTGACAATGTTAATCCATCGAATGATGAA
127 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGACAATGTTGATCCATCGAATGATGAA
*
74245 TTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
192 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
*
74288 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-C--G----GC-AATG-T--TGAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGCTAATGCTGATTAT
* * * * * * *
74341 C-CATCGAGTGATAAATTCAAGCAAAAAGTTGAACAAGTTC-T-T-ATTATTAACTTCTTC-TCC
65 CTCTTC-TG-GATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * * * *
74401 TTCTTCAGATGAGTTCTTCTTATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAAT
128 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGACAATGTTGATCCATCGAATGATGAAT
*
74466 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
193 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * **
74508 TCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAACCCT-TCTGGAAATG
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
74557 TTTTAAGAAA
Statistics
Matches: 655, Mismatches: 65, Indels: 64
0.84 0.08 0.08
Matches are distributed among these distances:
220 108 0.16
221 41 0.06
222 2 0.00
223 3 0.00
224 28 0.04
225 3 0.00
226 2 0.00
228 1 0.00
229 4 0.01
234 1 0.00
236 83 0.13
237 216 0.33
238 4 0.01
239 1 0.00
241 6 0.01
243 1 0.00
244 2 0.00
245 67 0.10
246 80 0.12
247 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (234 bp):
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATGCTGATTATC
TCTTCTGGATAGAGTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
TTCAGATGAGTTCTTCTCATTATGAACTCTACCTGACAATGTTGATCCATCGAATGATGAATTCA
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
Found at i:74429 original size:220 final size:225
Alignment explanation
Indices: 74133--74558 Score: 655
Period size: 220 Copynumber: 1.9 Consensus size: 225
74123 TGAAATAGAG
*
74133 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCT
* * *
74198 TCTCATTATGAACTCTACTTGACAATGTTAATCCATCGAATGATGAATTCAAGCAAAAAGTTGAA
66 TCTCATTATGAACTCGACCTGACAATGCTAATCCATCGAATGATGAATTCAAGCAAAAAGTTGAA
* *
74263 CAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTATGAACTCTT
131 CAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAAATGAGTTCTTCTCATTATGAACCCTT
*
74327 CCGGCAATGTTGATCCATCGAGTGATAAAT
196 CCGGAAATGTTGATCCATCGAGTGATAAAT
* * *
74357 TCAAGCAAAAAGTTGAACAAGTTC-T-T-ATTATTAACTTCTTC-TCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCT
* * * * * *
74418 TCTTATTATGAACTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAA
66 TCTCATTATGAACTCGACCTGACAATGCTAATCCATCGAATGATGAATTCAAGCAAAAAGTTGAA
*
74483 CAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCTCATTATGAACCCTT
131 CAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAAATGAGTTCTTCTCATTATGAACCCTT
*
74548 CTGGAAATGTT
196 CCGGAAATGTT
74559 TTAAGAAAAA
Statistics
Matches: 183, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
220 106 0.58
221 53 0.29
222 1 0.01
223 1 0.01
224 22 0.12
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (225 bp):
TCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCGACCTGACAATGCTAATCCATCGAATGATGAATTCAAGCAAAAAGTTGAA
CAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCTTCAAATGAGTTCTTCTCATTATGAACCCTT
CCGGAAATGTTGATCCATCGAGTGATAAAT
Found at i:75383 original size:22 final size:22
Alignment explanation
Indices: 75355--75475 Score: 197
Period size: 22 Copynumber: 5.5 Consensus size: 22
75345 GATAAAGCTT
75355 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
75377 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
75399 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
75421 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
75443 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
75465 TCATCTTTGAA
1 TCATCTTTGAA
75476 GAATGTAGAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 90 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:76849 original size:76 final size:74
Alignment explanation
Indices: 76630--76877 Score: 309
Period size: 75 Copynumber: 3.3 Consensus size: 74
76620 AGGATGATAT
* *
76630 GGGCCTTCAGCATGCCCCAACAATTGTTGATACGAACGTTCAAAATACATCAATATTCTTGATTC
1 GGGCTTTCAGCATGCCCCAACAATTGTTGATACGAACGTTCAAAATACATCAACATTCTTGATTC
76695 TGATTGAAATA
66 TGATT-AAA-A
* *
76706 -GGCTTTCAGCATGCCCCATCAATTGTTGATACGAACGTTCAAAATACATCAACATTCTTCATTC
1 GGGCTTTCAGCATGCCCCAACAATTGTTGATACGAACGTTCAAAATACATCAACATTCTTGATTC
76770 TGATTAAAA
66 TGATTAAAA
* * * ** * ** *
76779 GGGGCTTTCAGCATGCCCCAGCATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGAT
1 -GGGCTTTCAGCATGCCCCAACA-ATTGTTGATACGAACGTTCAAAATACATCAACATTCTTGAT
76844 TCTGATTGAAAA
64 TCTGATT-AAAA
* *
76856 GGGTTTTCAGCATGCCCTAACA
1 GGGCTTTCAGCATGCCCCAACA
76878 TTTGCTTCTT
Statistics
Matches: 151, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
73 1 0.01
74 3 0.02
75 85 0.56
76 58 0.38
77 4 0.03
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (74 bp):
GGGCTTTCAGCATGCCCCAACAATTGTTGATACGAACGTTCAAAATACATCAACATTCTTGATTC
TGATTAAAA
Found at i:79478 original size:32 final size:32
Alignment explanation
Indices: 79384--79480 Score: 176
Period size: 32 Copynumber: 3.0 Consensus size: 32
79374 GAAGAAATGA
* *
79384 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTTG
79416 TTGTTATGCTCATCTGGTAGAGATACTTCTTG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTTG
79448 TTGTTATGCTCATCTGGTAGAGATACTTCTTG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTTG
79480 T
1 T
79481 GTCTGACTCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTTG
Found at i:80107 original size:17 final size:17
Alignment explanation
Indices: 80087--80167 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
80077 CAATTTTTTC
80087 TTTTTTTTCCTTTTTAT
1 TTTTTTTTCCTTTTTAT
**
80104 TTTTTTTTTATTTTTAT
1 TTTTTTTTCCTTTTTAT
*
80121 TTCTTTTCTT--TTTTTCT
1 TT-TTTT-TTCCTTTTTAT
80138 TTTTTTTTCCTCTTTT-T
1 TTTTTTTTCCT-TTTTAT
*
80155 TCTTTTTTCCTTT
1 TTTTTTTTCCTTT
80168 CTTTGTTGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
15 2 0.04
16 6 0.11
17 37 0.67
18 8 0.15
19 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCCTTTTTAT
Found at i:80118 original size:33 final size:34
Alignment explanation
Indices: 80081--80167 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 34
80071 TTGATTCAAT
80081 TTTTTCTTTTTTTTCCTTTTTAT-TTTTTTTTT-A
1 TTTTT-TTTTTTTTCCTTTTTATCTTTTTTTTTCA
* * *
80114 TTTTTATTTCTTTT-CTTTTTTTCTTTTTTTTTCC
1 TTTTT-TTTTTTTTCCTTTTTATCTTTTTTTTTCA
80148 TCTTTTTTCTTTTTTCCTTT
1 T-TTTTTT-TTTTTTCCTTT
80168 CTTTGTTGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
32 7 0.16
33 21 0.48
34 3 0.07
35 9 0.20
36 4 0.09
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (34 bp):
TTTTTTTTTTTTTCCTTTTTATCTTTTTTTTTCA
Found at i:80162 original size:1 final size:1
Alignment explanation
Indices: 80080--80145 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
80070 CTTGATTCAA
* ** * * * * * *
80080 TTTTTTCTTTTTTTTCCTTTTTATTTTTTTTTTATTTTTATTTCTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
80145 T
1 T
80146 CCTCTTTTTT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:80163 original size:27 final size:26
Alignment explanation
Indices: 80080--80163 Score: 88
Period size: 25 Copynumber: 3.3 Consensus size: 26
80070 CTTGATTCAA
80080 TTTTTTC-TTTTTTTTCCT-TTTTATT
1 TTTTTTCTTTTTTTTTCCTCTTTT-TT
*
80105 TTTTTT-TTATTTTTATT--TCTTTTCT
1 TTTTTTCTT-TTTTT-TTCCTCTTTTTT
80130 TTTTTTCTTTTTTTTTCCTCTTTTTT
1 TTTTTTCTTTTTTTTTCCTCTTTTTT
80156 CTTTTTTC
1 -TTTTTTC
80164 CTTTCTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 2 0.04
25 20 0.41
26 18 0.37
27 9 0.18
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTTCTTTTTTTTTCCTCTTTTTT
Found at i:80181 original size:27 final size:26
Alignment explanation
Indices: 80151--80204 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
80141 TTTTTCCTCT
80151 TTTTTCTTTTTTCCTTTCTTTGTTGGA
1 TTTTTCTTTTTT-CTTTCTTTGTTGGA
80178 TTTTTCTTTTTTCTTTCTTTGTTGGA
1 TTTTTCTTTTTTCTTTCTTTGTTGGA
80204 T
1 T
80205 GAGTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGTTGGA
Found at i:80498 original size:2 final size:2
Alignment explanation
Indices: 80491--80548 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
80481 ACAACAAAGG
80491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80533 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
80549 TAAAGGATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82757 original size:12 final size:12
Alignment explanation
Indices: 82738--82786 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
82728 GTAAAAATGA
82738 AAATGTAAATAC
1 AAATGTAAATAC
* *
82750 AAACGTAAAAATGC
1 AAATGT--AAATAC
*
82764 AAATGTAAATGC
1 AAATGTAAATAC
82776 AAATGTAAATA
1 AAATGTAAATA
82787 TGTGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:82797 original size:26 final size:26
Alignment explanation
Indices: 82728--82784 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
82718 ATGTAATTAT
*
82728 GTAAAAATGAAAATGTAAATACAAAC
1 GTAAAAATGCAAATGTAAATACAAAC
* *
82754 GTAAAAATGCAAATGTAAATGCAAAT
1 GTAAAAATGCAAATGTAAATACAAAC
82780 GTAAA
1 GTAAA
82785 TATGTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (26 bp):
GTAAAAATGCAAATGTAAATACAAAC
Found at i:82878 original size:7 final size:7
Alignment explanation
Indices: 82844--82885 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
82834 ATAAAAGTAT
82844 AAATGCA
1 AAATGCA
* *
82851 CAATGAA
1 AAATGCA
82858 AAATGCA
1 AAATGCA
82865 AAGATGCA
1 AA-ATGCA
82873 AAATGC-
1 AAATGCA
82879 AAATGCA
1 AAATGCA
82886 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:85249 original size:11 final size:11
Alignment explanation
Indices: 85233--85259 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
85223 ATATGACTAA
85233 AATAAAATAAT
1 AATAAAATAAT
85244 AATAAAATAAT
1 AATAAAATAAT
85255 AATAA
1 AATAA
85260 TTAAAGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:86639 original size:10 final size:10
Alignment explanation
Indices: 86624--86650 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
86614 GGGGCTGCTC
86624 GCTGGAAGCT
1 GCTGGAAGCT
86634 GCTGGAAGCT
1 GCTGGAAGCT
86644 GCTGGAA
1 GCTGGAA
86651 ATGATGCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (10 bp):
GCTGGAAGCT
Found at i:87661 original size:20 final size:20
Alignment explanation
Indices: 87633--87687 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
87623 GTGTCGGTAT
*
87633 TGTAAGAACAATATCGATAA
1 TGTAAGAACAATACCGATAA
* *
87653 TGTATGAACAATACCGATAC
1 TGTAAGAACAATACCGATAA
87673 TGTAAGAACAATACC
1 TGTAAGAACAATACC
87688 AATATTGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
TGTAAGAACAATACCGATAA
Found at i:87966 original size:18 final size:19
Alignment explanation
Indices: 87945--87996 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
87935 GCTAAAATTG
* *
87945 GTATCTATACTAAGGC-CA
1 GTATCGATACTAAGACTCA
87963 GTATCGATACTGACAGACTCA
1 GTATCGATACT-A-AGACTCA
87984 GTATCGATACTAA
1 GTATCGATACTAA
87997 TGGACTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (19 bp):
GTATCGATACTAAGACTCA
Found at i:88002 original size:21 final size:20
Alignment explanation
Indices: 87945--88002 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
87935 GCTAAAATTG
*
87945 GTATCTATACTAAGG-C-CA
1 GTATCGATACTAAGGACTCA
87963 GTATCGATACTGACA-GACTCA
1 GTATCGATACT-A-AGGACTCA
87984 GTATCGATACTAATGGACT
1 GTATCGATACTAA-GGACT
88003 GTTTTCGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 10 0.30
19 3 0.09
20 3 0.09
21 17 0.52
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
GTATCGATACTAAGGACTCA
Found at i:89468 original size:9 final size:9
Alignment explanation
Indices: 89454--89481 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
89444 TGATTGTATG
89454 ATTGGTTGA
1 ATTGGTTGA
89463 ATTGGTTGA
1 ATTGGTTGA
89472 ATTGGTTGA
1 ATTGGTTGA
89481 A
1 A
89482 CTCCATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (9 bp):
ATTGGTTGA
Found at i:91681 original size:24 final size:24
Alignment explanation
Indices: 91624--91671 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
91614 ATTATTTTCA
91624 ATCTTAATTTATGTTTCCTTTTAT
1 ATCTTAATTTATGTTTCCTTTTAT
91648 ATCTTAATTTATGTTTCCTTTTAT
1 ATCTTAATTTATGTTTCCTTTTAT
91672 TTTACAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.62
Consensus pattern (24 bp):
ATCTTAATTTATGTTTCCTTTTAT
Done.