Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004744.1 Hibiscus syriacus cultivar Beakdansim tig00010706_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: 77107
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:880 original size:54 final size:55
Alignment explanation
Indices: 709--937 Score: 245
Period size: 52 Copynumber: 4.1 Consensus size: 55
699 CTACAGGAGG
* * *
709 TGGTGGTGGAGGAAGTGCTGCTGCTGTTACCTCTATATTTGGCTCTGTTGGAGCTGC
1 TGGTGGTGGAGG-AGAG-TGCTGCTGTTACCTCTATATTTGGCTCTGTTGCAGCTGA
* * *
766 TGCTGGTGGAGG-GAGTGCTGCTGTTACCTC--TATTTGGCCCTGTTGGAGCTGA
1 TGGTGGTGGAGGAGAGTGCTGCTGTTACCTCTATATTTGGCTCTGTTGCAGCTGA
* *
818 TGGTGGTGGAGGAG-GTTCTGCTGTTACCTCTATGTTTGGCTCTGGTTGCA-CTGA
1 TGGTGGTGGAGGAGAGTGCTGCTGTTACCTCTATATTTGGCTCT-GTTGCAGCTGA
* * *
872 TGGTGGTGGTGGTGGAGGTTCTGCTGCTGCTACCTCTATATTTGGCTCTGTTGC-GCTGA
1 TGGTGGTGGAGG-AGA-G---TGCTGCTGTTACCTCTATATTTGGCTCTGTTGCAGCTGA
931 TGGTGGT
1 TGGTGGT
938 AGTGATGGTG
Statistics
Matches: 147, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
52 46 0.31
53 1 0.01
54 39 0.27
55 8 0.05
57 12 0.08
59 16 0.11
60 25 0.17
ACGTcount: A:0.10, C:0.17, G:0.36, T:0.36
Consensus pattern (55 bp):
TGGTGGTGGAGGAGAGTGCTGCTGTTACCTCTATATTTGGCTCTGTTGCAGCTGA
Found at i:887 original size:60 final size:59
Alignment explanation
Indices: 707--964 Score: 218
Period size: 52 Copynumber: 4.5 Consensus size: 59
697 CACTACAGGA
*
707 GGTGGTGGTGGAGGAAGTGCTGCTGCTGTTACCTCTATATTTGGCTCTGTTG----GA-GCT
1 GGTGGTGGTGGAGG-AG-G-TGCTGCTGTTACCTCTATATTTGGCTCTGTTGCACTGATGGT
* * * *
764 GCTGCTGGTGGAGG-GAGTGCTGCTGTTACCTC--TATTTGGCCCTGTTG----GA-GCT
1 GGTGGTGGTGGAGGAG-GTGCTGCTGTTACCTCTATATTTGGCTCTGTTGCACTGATGGT
* * *
816 GATGGTGGTGGAGGAGGTTCTGCTGTTACCTCTATGTTTGGCTCTGGTTGCACTGATGGT
1 GGTGGTGGTGGAGGAGGTGCTGCTGTTACCTCTATATTTGGCTCT-GTTGCACTGATGGT
*** * *
876 GGTGGTGGTGGAGGTTCTGCTGCTGCTACCTCTATATTTGGCTCTGTTGCGCTGATGGT
1 GGTGGTGGTGGAGGAGGTGCTGCTGTTACCTCTATATTTGGCTCTGTTGCACTGATGGT
* *
935 GGTAGTGATGGTGGTGGAGGTGGTGCTGTT
1 GGT-G-G-TGGTGGAGGAGGTGCTGCTGTT
965 GCTGTTACCC
Statistics
Matches: 165, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
52 46 0.28
53 1 0.01
54 24 0.15
55 6 0.04
57 12 0.07
59 18 0.11
60 41 0.25
61 1 0.01
62 16 0.10
ACGTcount: A:0.10, C:0.16, G:0.38, T:0.35
Consensus pattern (59 bp):
GGTGGTGGTGGAGGAGGTGCTGCTGTTACCTCTATATTTGGCTCTGTTGCACTGATGGT
Found at i:8969 original size:53 final size:52
Alignment explanation
Indices: 8887--8993 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 52
8877 ATCATGGATG
*
8887 AATTTAAAAGAAATTTCAAGTCCATATATTAATTTAAGAAAAGATTTATGTATC
1 AATTTAAAAGAAATTTCAAGTCCAGATATTAATTTAAG-AAA-ATTTATGTATC
* *
8941 AATTTAAGA-AAATTTCAAGTCTAGATATTAATTTAAGAAAATTTATGTATC
1 AATTTAAAAGAAATTTCAAGTCCAGATATTAATTTAAGAAAATTTATGTATC
8992 AA
1 AA
8994 GTCTAGTCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 13 0.26
52 3 0.06
53 26 0.52
54 8 0.16
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (52 bp):
AATTTAAAAGAAATTTCAAGTCCAGATATTAATTTAAGAAAATTTATGTATC
Found at i:9436 original size:69 final size:67
Alignment explanation
Indices: 9339--9568 Score: 217
Period size: 63 Copynumber: 3.5 Consensus size: 67
9329 TCATACATAT
* * * * **
9339 ATAAGTAATAATACGACACATGTCATGTGTACAAACTATAAAGTGATGAATTGGTAAATGCTACA
1 ATAAGTGATGATATGACACATGTCATGTGTACAAAC---AAAGTGATAAATTGACAAATGCTACA
9404 TGTAC
63 TGTAC
* * *
9409 ATAAGT-ATGATGTGACACATGTCATGTGT----ACGAAGTGATAAATTGACACATGCTACATGT
1 ATAAGTGATGATATGACACATGTCATGTGTACAAACAAAGTGATAAATTGACAAATGCTACATGT
9469 AC
66 AC
* * * ** *
9471 ATAAGTGATGGTATGACACATGTCGTGTGTAC--A-AAA-CGATAACGTGACATATGCTACATGT
1 ATAAGTGATGATATGACACATGTCATGTGTACAAACAAAGTGATAAATTGACAAATGCTACATGT
9532 AC
66 AC
* *
9534 ACAAGTGATGATATGATACATGTCATGTGTACAAA
1 ATAAGTGATGATATGACACATGTCATGTGTACAAA
9569 ATGATCACCC
Statistics
Matches: 135, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
62 32 0.24
63 71 0.53
64 2 0.01
65 4 0.03
69 20 0.15
70 6 0.04
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (67 bp):
ATAAGTGATGATATGACACATGTCATGTGTACAAACAAAGTGATAAATTGACAAATGCTACATGT
AC
Found at i:9439 original size:31 final size:32
Alignment explanation
Indices: 9404--9566 Score: 108
Period size: 32 Copynumber: 5.2 Consensus size: 32
9394 AAATGCTACA
*
9404 TGTACATAAGT-ATGATGTGACACATGTCATG
1 TGTACATAAGTGATGATATGACACATGTCATG
* *
9435 TGTAC-GAAGTGAT-AAATTGACACATGCTACA--
1 TGTACATAAGTGATGATA-TGACACATG-T-CATG
* *
9466 TGTACATAAGTGATGGTATGACACATGTCGTG
1 TGTACATAAGTGATGATATGACACATGTCATG
** * ** *
9498 TGTACA-AAACGATAACGTGACATATGCTACA--
1 TGTACATAAGTGATGATATGACACATG-T-CATG
* *
9529 TGTACACAAGTGATGATATGATACATGTCATG
1 TGTACATAAGTGATGATATGACACATGTCATG
9561 TGTACA
1 TGTACA
9567 AAATGATCAC
Statistics
Matches: 97, Mismatches: 22, Indels: 25
0.67 0.15 0.17
Matches are distributed among these distances:
30 8 0.08
31 42 0.43
32 43 0.44
33 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (32 bp):
TGTACATAAGTGATGATATGACACATGTCATG
Found at i:9488 original size:32 final size:32
Alignment explanation
Indices: 9396--9555 Score: 102
Period size: 31 Copynumber: 5.1 Consensus size: 32
9386 GAATTGGTAA
*
9396 ATGCTACATGTACATAAGT-ATGATGTGACAC
1 ATGCTACATGTACATAAGTGATGATATGACAC
* *
9427 ATG-T-CATGTGTAC-GAAGTGAT-AAATTGACAC
1 ATGCTACA--TGTACATAAGTGATGATA-TGACAC
*
9458 ATGCTACATGTACATAAGTGATGGTATGACAC
1 ATGCTACATGTACATAAGTGATGATATGACAC
* ** * ** *
9490 ATG-T-CGTGTGTACA-AAACGATAACGTGACAT
1 ATGCTAC--ATGTACATAAGTGATGATATGACAC
* *
9521 ATGCTACATGTACACAAGTGATGATATGATAC
1 ATGCTACATGTACATAAGTGATGATATGACAC
9553 ATG
1 ATG
9556 TCATGTGTAC
Statistics
Matches: 94, Mismatches: 22, Indels: 25
0.67 0.16 0.18
Matches are distributed among these distances:
29 2 0.02
30 7 0.07
31 44 0.47
32 37 0.39
33 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (32 bp):
ATGCTACATGTACATAAGTGATGATATGACAC
Found at i:9519 original size:63 final size:63
Alignment explanation
Indices: 9396--9569 Score: 242
Period size: 63 Copynumber: 2.8 Consensus size: 63
9386 GAATTGGTAA
* * ** *
9396 ATGCTACATGTACATAAGT-ATGATGTGACACATGTCATGTGTACGAAGTGATAAATTGACAC
1 ATGCTACATGTACATAAGTGATGATATGACACATGTCATGTGTACAAAACGATAAAGTGACAC
* * * *
9458 ATGCTACATGTACATAAGTGATGGTATGACACATGTCGTGTGTACAAAACGATAACGTGACAT
1 ATGCTACATGTACATAAGTGATGATATGACACATGTCATGTGTACAAAACGATAAAGTGACAC
* *
9521 ATGCTACATGTACACAAGTGATGATATGATACATGTCATGTGTACAAAA
1 ATGCTACATGTACATAAGTGATGATATGACACATGTCATGTGTACAAAA
9570 TGATCACCCG
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
62 19 0.19
63 79 0.81
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (63 bp):
ATGCTACATGTACATAAGTGATGATATGACACATGTCATGTGTACAAAACGATAAAGTGACAC
Found at i:17256 original size:6 final size:6
Alignment explanation
Indices: 17245--17269 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17235 TATCAAGTAA
17245 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
17270 TATATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:17865 original size:42 final size:43
Alignment explanation
Indices: 17814--17972 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 43
17804 AGGATTTAAT
17814 TTTTTTTAATATCACTTTTTATCTTTATAATTGAGGCTCCT-A
1 TTTTTTTAATATCACTTTTTATCTTTATAATTGAGGCTCCTAA
* * * *
17856 TTTTTTTAATATCACTTTCTATCTTTATAATCGAGGCTCTTGA
1 TTTTTTTAATATCACTTTTTATCTTTATAATTGAGGCTCCTAA
* *
17899 TTTTTTTAATCTCACATTTTAT-TTTATAATTGAGG-TCCCTAA
1 TTTTTTTAATATCACTTTTTATCTTTATAATTGAGGCT-CCTAA
* ** *
17941 TTTTTTCAACCTCACTTCTTA-CTTTTATAATT
1 TTTTTTTAATATCACTTTTTATC-TTTATAATT
17973 TTTGTCCCTA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.70
43 29 0.29
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.53
Consensus pattern (43 bp):
TTTTTTTAATATCACTTTTTATCTTTATAATTGAGGCTCCTAA
Found at i:18482 original size:19 final size:19
Alignment explanation
Indices: 18441--18484 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
18431 TCATATTTTT
*
18441 ATATTATACATATCATATT
1 ATATTATACATATCATATC
*
18460 ATATTATACTTAT-ATATGC
1 ATATTATACATATCATAT-C
18479 ATATTA
1 ATATTA
18485 AATATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTATACATATCATATC
Found at i:18490 original size:23 final size:23
Alignment explanation
Indices: 18450--18496 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
18440 TATATTATAC
*
18450 ATATCATATTATATTATACTTAT
1 ATATCATATTATAATATACTTAT
*
18473 ATATGCATATTA-AATATATTTAT
1 ATAT-CATATTATAATATACTTAT
18496 A
1 A
18497 CATTGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATCATATTATAATATACTTAT
Found at i:19565 original size:2 final size:2
Alignment explanation
Indices: 19560--19595 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19550 AAAATTTCAA
19560 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
19596 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20474 original size:28 final size:31
Alignment explanation
Indices: 20438--20495 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
20428 ACACTTCTTA
20438 AATATTTATAAACAT-T-AAAAATTATAATT
1 AATATTTATAAACATATAAAAAATTATAATT
20467 AATA-TTATAAACATAATAAAAAATTATAA
1 AATATTTATAAACAT-ATAAAAAATTATAA
20496 GAAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 10 0.38
29 4 0.15
30 1 0.04
31 11 0.42
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
AATATTTATAAACATATAAAAAATTATAATT
Found at i:20522 original size:15 final size:16
Alignment explanation
Indices: 20489--20524 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20479 ATAATAAAAA
20489 ATTATAAGAAAACTAT
1 ATTATAAGAAAACTAT
*
20505 ATTATAAGCAAA-TAT
1 ATTATAAGAAAACTAT
20520 ATTAT
1 ATTAT
20525 GGCTTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTATAAGAAAACTAT
Found at i:24771 original size:21 final size:23
Alignment explanation
Indices: 24747--24798 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
24737 GGGTGAACTG
*
24747 TAGATATATTTATAT-TAAT-AA
1 TAGAAATATTTATATATAATGAA
*
24768 TAGAAATTTTTATATATAATGAA
1 TAGAAATATTTATATATAATGAA
*
24791 TATAAATA
1 TAGAAATA
24799 AAATTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 4 0.16
23 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
TAGAAATATTTATATATAATGAA
Found at i:24792 original size:23 final size:21
Alignment explanation
Indices: 24755--24797 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
24745 TGTAGATATA
24755 TTTATATTAATAATAGAAATT
1 TTTATATTAATAATAGAAATT
*
24776 TTTATATATAATGAATATAAAT
1 TTTATAT-TAAT-AATAGAAAT
24798 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTATATTAATAATAGAAATT
Found at i:30074 original size:2 final size:2
Alignment explanation
Indices: 30067--30094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30057 AGCTACCAAT
30067 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
30095 GTATTAGCCA
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):
TA
Found at i:30623 original size:2 final size:2
Alignment explanation
Indices: 30616--30655 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
30606 GCGTGTAAAT
*
30616 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GG GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30656 CTGGTAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34940 original size:37 final size:37
Alignment explanation
Indices: 34898--35217 Score: 184
Period size: 37 Copynumber: 8.8 Consensus size: 37
34888 CCAAAATGCT
* * *
34898 TTTTAAAAACTATATATTATACATGTTTTTAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * * * *
34935 TTTTAAAAA-T-TTTATAATATATATTTTCAGAAACG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * *
34970 GTTT-AAAATTACATATTATATAT-TTTTT-AAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * * *
35004 TTTTTCAAAAATTATATAATATTTAAATGTTTTTAAAAA--
1 -TTTT-AAAAACTATAT-AT-TATATATATTTTTAAAAATG
** * * *
35043 AATTCAAAACAATATATTATATA-ATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* *
35079 ATTTTAAAAATTATATATTATATATATTTCT-AAAATG
1 -TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * *
35116 TTTT-AAAAC--TATA-TATATATAGTTTCAACAAATA
1 TTTTAAAAACTATATATTATATATATTTTTAA-AAATG
* * *
35150 TTTTTAAAACTATATATTATATACA-TTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
*
35186 TTTTCAAAAATTATGTATATTATA-AGTATTTT
1 TTTT-AAAAACTA--TATATTATATA-TATTTT
35218 CAAAGACCGT
Statistics
Matches: 214, Mismatches: 45, Indels: 45
0.70 0.15 0.15
Matches are distributed among these distances:
32 10 0.05
33 5 0.02
34 25 0.12
35 43 0.20
36 24 0.11
37 64 0.30
38 16 0.07
39 15 0.07
40 8 0.04
41 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTTAAAAATG
Found at i:35046 original size:30 final size:30
Alignment explanation
Indices: 34984--35043 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
34974 AAAATTACAT
* * *
34984 ATTATATATTTTTTAAAATGTTTTTCAAAA
1 ATTATATAATATTTAAAATGTTTTTAAAAA
35014 ATTATATAATATTT-AAATGTTTTTAAAAA
1 ATTATATAATATTTAAAATGTTTTTAAAAA
35043 A
1 A
35044 ATTCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTATATAATATTTAAAATGTTTTTAAAAA
Found at i:35155 original size:35 final size:35
Alignment explanation
Indices: 35048--35183 Score: 150
Period size: 35 Copynumber: 3.8 Consensus size: 35
35038 AAAAAAATTC
* *
35048 AAAACAATATATTATATAATTTTCAAAAATGATTTTA
1 AAAACTATATATTATATAA-TTTCAAAAAT-ATTTTT
* * *
35085 AAAATTATATATTATATATATTTCTAAAAT-GTTTT
1 AAAACTATATATTATATA-ATTTCAAAAATATTTTT
*
35120 AAAACTATATA-TATATAGTTTCAACAAATATTTTT
1 AAAACTATATATTATATAATTTCAA-AAATATTTTT
35155 AAAACTATATATTATATACATTTTCAAAA
1 AAAACTATATATTATATA-A-TTTCAAAA
35184 TGTTTTCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
33 5 0.06
34 10 0.12
35 28 0.34
36 6 0.07
37 27 0.33
38 7 0.08
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (35 bp):
AAAACTATATATTATATAATTTCAAAAATATTTTT
Found at i:35164 original size:70 final size:73
Alignment explanation
Indices: 35045--35194 Score: 202
Period size: 70 Copynumber: 2.1 Consensus size: 73
35035 TTTAAAAAAA
* * *
35045 TTCAAAACAATATATTATATAATTTTCAAAAATGATTTTAAAAATTATATATTATATATA-TTTC
1 TTCAAAACAATATATTATATAAGTTTCAAAAATGATTTTAAAAACTATATATTATATACATTTTC
35109 TAAAATGTT
66 -AAAATGTT
* *
35118 TT-AAAACTATATA-TATAT-AGTTTCAACAAAT-ATTTTTAAAACTATATATTATATACATTTT
1 TTCAAAACAATATATTATATAAGTTTCAA-AAATGATTTTAAAAACTATATATTATATACATTTT
35179 CAAAATGTT
65 CAAAATGTT
35188 TTCAAAA
1 TTCAAAA
35195 ATTATGTATA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
70 40 0.58
71 17 0.25
72 10 0.14
73 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (73 bp):
TTCAAAACAATATATTATATAAGTTTCAAAAATGATTTTAAAAACTATATATTATATACATTTTC
AAAATGTT
Found at i:36069 original size:165 final size:165
Alignment explanation
Indices: 35876--36633 Score: 1232
Period size: 164 Copynumber: 4.6 Consensus size: 165
35866 AAGTTGAATA
* *
35876 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
35941 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
*
36006 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
* *
36041 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
36106 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
*
36171 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
* * * *
36206 TAATCGAACTCGGGGGTCTTTGGCAGATGGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
36271 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
* *
36335 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
** * *
36370 TAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
36435 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-CTAACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
* * *
36499 TTATGCTGAAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
** *
36534 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
36599 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
36634 GGTGGCAGGT
Statistics
Matches: 565, Mismatches: 27, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
164 310 0.55
165 255 0.45
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
Found at i:40039 original size:20 final size:21
Alignment explanation
Indices: 40011--40049 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40001 AATGTGAATG
*
40011 AAGAGAAAATAATAAAATGCA
1 AAGAGAAAATAAAAAAATGCA
40032 AAGA-AAAATAAAAAAATG
1 AAGAGAAAATAAAAAAATG
40050 TAAAATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.03, G:0.13, T:0.13
Consensus pattern (21 bp):
AAGAGAAAATAAAAAAATGCA
Found at i:43049 original size:37 final size:37
Alignment explanation
Indices: 43007--43332 Score: 224
Period size: 37 Copynumber: 8.8 Consensus size: 37
42997 CCAAAATGCT
* * *
43007 TTTTAAAAACTATATATTATACATGTTTTTAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * * * *
43044 TTTTAAAAA-T-TTTATAATATATATTTTCAGAAACG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * *
43079 GTTTAAAAATTACATATTATATATATTTTT-AAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
* * * *
43115 TTTTTCAAAAATTATATAATATTTAAATGTTTTTAAAAA--
1 -TTTT-AAAAACTATAT-AT-TATATATATTTTTAAAAATG
** * *
43154 AATTCAAAACAATATATTATATA-ATTTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTT-AAAAATG
*
43191 ATTTTAAAAATTATATATTATATATATTTTCT-AAAATG
1 -TTTTAAAAACTATATATTATATATATTTT-TAAAAATG
* * *
43229 TTTTAAAAACTATATA--ATATATAGTTTCAACAAATA
1 TTTTAAAAACTATATATTATATATATTTTTAA-AAATG
* * *
43265 TTTTTAAAACTATATATTATATACA-TTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTTAAAAATG
*
43301 TTTTCAAAAATTATGTATATTATA-AGTATTTT
1 TTTT-AAAAACTA--TATATTATATA-TATTTT
43333 CAAAGACCGT
Statistics
Matches: 224, Mismatches: 43, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
34 5 0.02
35 47 0.21
36 35 0.16
37 59 0.26
38 43 0.19
39 17 0.08
40 14 0.06
41 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTTAAAAATG
Found at i:43084 original size:35 final size:36
Alignment explanation
Indices: 43039--43107 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
43029 ATGTTTTTAA
* *
43039 AAACGTTTTAAAAATT-TTATAATATATATTTTCAG
1 AAACGGTTTAAAAATTAATATAATATATATTTTCAG
*
43074 AAACGGTTTAAAAATTACATATTATATATATTTT
1 AAACGGTTTAAAAATTA-ATATAATATATATTTT
43108 TAAAATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 15 0.52
37 14 0.48
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
AAACGGTTTAAAAATTAATATAATATATATTTTCAG
Found at i:43142 original size:29 final size:31
Alignment explanation
Indices: 43094--43154 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
43084 AAAATTACAT
* *
43094 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTTAAAAA
43125 ATTATATA-ATATTT-AAATGTTTTTAAAAA
1 ATTATATATATATTTAAAATGTTTTTAAAAA
43154 A
1 A
43155 ATTCAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 5 0.18
31 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTTAAAAA
Found at i:46733 original size:14 final size:14
Alignment explanation
Indices: 46701--46727 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46691 AATGAATTAC
46701 ATTTTCTGAAAAAT
1 ATTTTCTGAAAAAT
46715 ATTTTCTGAAAAA
1 ATTTTCTGAAAAA
46728 AGTTTTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTTTCTGAAAAAT
Found at i:47029 original size:23 final size:23
Alignment explanation
Indices: 47001--47045 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46991 GATATTATAT
47001 TATATTTTAAAAATCTTAATTAG
1 TATATTTTAAAAATCTTAATTAG
* *
47024 TATATTTTAAATATCTTTATTA
1 TATATTTTAAAAATCTTAATTA
47046 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATCTTAATTAG
Found at i:47051 original size:23 final size:23
Alignment explanation
Indices: 47002--47052 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
46992 ATATTATATT
**
47002 ATATTTTAAAAATCTTAATTAGT
1 ATATTTTAAAAATCTTAATTAAA
* *
47025 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATCTTAATTAAA
47048 ATATT
1 ATATT
47053 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATCTTAATTAAA
Found at i:47108 original size:19 final size:19
Alignment explanation
Indices: 47040--47108 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
47030 TTAAATATCT
47040 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
47059 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
47078 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
47098 TTATTAATAAT
1 TTATTAATAAT
47109 TTAAATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:47216 original size:54 final size:52
Alignment explanation
Indices: 47158--47259 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 52
47148 AATTTTACTA
*
47158 ATAATTTATTATATATTATTAA-AATAAAAATATAATATCTTATATTATTATAAT
1 ATAATTGATTATATATTA-TAATAATAAAAATATAATA--TTATATTATTATAAT
* *
47212 ATAATTGATTATTTATTATAATATTAAAAATATAATATTATATTATTA
1 ATAATTGATTATATATTATAATAATAAAAATATAATATTATATTATTA
47260 GAAATATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 11 0.25
53 3 0.07
54 30 0.68
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
ATAATTGATTATATATTATAATAATAAAAATATAATATTATATTATTATAAT
Found at i:47247 original size:31 final size:32
Alignment explanation
Indices: 47199--47277 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
47189 ATAATATCTT
* *
47199 ATATTATTATAATATAATTGATTAT-TTATTA-TA
1 ATATTAATA-AATATAA-T-ATTATATTATTAGAA
47232 ATATTAA-AAATATAATATTATATTATTAGAA
1 ATATTAATAAATATAATATTATATTATTAGAA
47263 ATATTAATAAATATA
1 ATATTAATAAATATA
47278 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 5 0.12
30 7 0.17
31 15 0.37
32 8 0.20
33 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATATTAATAAATATAATATTATATTATTAGAA
Found at i:47250 original size:22 final size:23
Alignment explanation
Indices: 47225--47271 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
47215 ATTGATTATT
47225 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
47247 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
47270 TA
1 TA
47272 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:47272 original size:26 final size:24
Alignment explanation
Indices: 47243--47305 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
47233 TATTAAAAAT
47243 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
47269 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
47292 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
47306 GATTAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:47276 original size:22 final size:22
Alignment explanation
Indices: 47233--47276 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
47223 TTTATTATAA
*
47233 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
47255 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
47277 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:51787 original size:14 final size:13
Alignment explanation
Indices: 51768--51806 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
51758 TTGTTTCACG
*
51768 GAAAATAAATTCTA
1 GAAAATGAATT-TA
51782 GAAAATGAATTTA
1 GAAAATGAATTTA
51795 GTAAAATGAATT
1 G-AAAATGAATT
51807 ACATTTCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (13 bp):
GAAAATGAATTTA
Found at i:51995 original size:18 final size:18
Alignment explanation
Indices: 51943--52002 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
51933 TTTTATTAGA
51943 AAAT-AATATTATTATTTTT
1 AAATAAATATTATTA--TTT
*
51962 AAATAAA-ATAATTTATTT
1 AAATAAATATTA-TTATTT
* *
51980 AAGTAAATATTATTATTA
1 AAATAAATATTATTATTT
51998 AAATA
1 AAATA
52003 TTTTTCTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 18 0.55
19 10 0.30
20 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATAAATATTATTATTT
Found at i:52091 original size:14 final size:14
Alignment explanation
Indices: 52044--52091 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
52034 AGACTTATAT
*
52044 TTATTAAAATAAAA
1 TTATTAAAATAATA
* *
52058 TTTTTATAAATTAT-
1 TTATTA-AAATAATA
52072 TTATTAAAATAATA
1 TTATTAAAATAATA
52086 TTATTA
1 TTATTA
52092 TATTATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 6 0.22
14 16 0.59
15 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATTAAAATAATA
Found at i:52110 original size:26 final size:28
Alignment explanation
Indices: 52067--52119 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
52057 ATTTTTATAA
*
52067 ATTATTTATTAAAATAA-TA-TTATTAT
1 ATTATTAATTAAAATAATTACTTATTAT
* *
52093 ATTATTAATTATATTAATTACTTATTA
1 ATTATTAATTAAAATAATTACTTATTA
52120 AAATAAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
27 2 0.09
28 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTATTAATTAAAATAATTACTTATTAT
Found at i:53965 original size:31 final size:32
Alignment explanation
Indices: 53903--53971 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
53893 AATATCTATC
** *
53903 AAAAAATTTAAATATTTATTATTAATGAATTA
1 AAAAAATTTAAATAAATATTATTAATAAATTA
53935 AAAAAATTTCAAATAAATATTA-TAA-AAATTA
1 AAAAAATTT-AAATAAATATTATTAATAAATTA
*
53966 ATAAAA
1 AAAAAA
53972 GAGAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.31
32 12 0.38
33 10 0.31
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAAAATTTAAATAAATATTATTAATAAATTA
Found at i:54379 original size:2 final size:2
Alignment explanation
Indices: 54372--54413 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54362 AGTCCATAAC
54372 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
54414 GTTTATGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55352 original size:60 final size:60
Alignment explanation
Indices: 55241--55354 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
55231 CTATAGGATA
* * * *
55241 TTATTTTGTAGAGTCGATCGACTATTAAAAGTTATAAAGCAGTCCTCCAACTATAGAGAG
1 TTATTTTGTAGAGTCCATCAACTATTAAAAGTTATAAAACAATCCTCCAACTATAGAGAG
* * * *
55301 TTATTTTGTTGAGTCCCTCAACTATTAAAATTTATAAAATAATCACT-CAACTAT
1 TTATTTTGTAGAGTCCATCAACTATTAAAAGTTATAAAACAATC-CTCCAACTAT
55355 TCATTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
60 43 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (60 bp):
TTATTTTGTAGAGTCCATCAACTATTAAAAGTTATAAAACAATCCTCCAACTATAGAGAG
Found at i:68251 original size:17 final size:17
Alignment explanation
Indices: 68229--68262 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
68219 TGATTAAGCA
68229 CTGAATGATTCAATGGC
1 CTGAATGATTCAATGGC
68246 CTGAATGATTCAATGGC
1 CTGAATGATTCAATGGC
68263 TCTGTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
CTGAATGATTCAATGGC
Found at i:68588 original size:22 final size:22
Alignment explanation
Indices: 68541--68588 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
68531 CGCTGAATGT
* *
68541 TGAACGGTTCAGCATTCAACGT
1 TGAACGGTTCAACATTCAACGC
**
68563 TGAACGGTTCAACATTCGGCGC
1 TGAACGGTTCAACATTCAACGC
68585 TGAA
1 TGAA
68589 TCGTTCCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
TGAACGGTTCAACATTCAACGC
Found at i:68739 original size:2 final size:2
Alignment explanation
Indices: 68730--68759 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
68720 AGATAACGGA
68730 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68760 CGGGGTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71078 original size:84 final size:85
Alignment explanation
Indices: 70937--71105 Score: 313
Period size: 84 Copynumber: 2.0 Consensus size: 85
70927 AAAGTAAATC
*
70937 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATT-AACGTT
1 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
71001 CATCTTCTTACCTTGTACAA
66 CATCTTCTTACCTTGTACAA
*
71021 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCTCATACAATTAAAAGTT
1 TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
71086 CATCTTCTTACCTTGTACAA
66 CATCTTCTTACCTTGTACAA
71106 ATTCCAATAC
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
84 57 0.70
85 25 0.30
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (85 bp):
TAAAAGTCTCAATTCTTGGGACCATCCATTATCTATTAATACATCAGCCCATACAATTAAAAGTT
CATCTTCTTACCTTGTACAA
Done.