Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001894.1 Hibiscus syriacus cultivar Beakdansim tig00003840_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: 76155
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:964 original size:40 final size:39
Alignment explanation
Indices: 920--1050 Score: 174
Period size: 40 Copynumber: 3.3 Consensus size: 39
910 AATTTCCAAT
*
920 TTCGCAACGCGAATCTGTAAATCGTAACACAAAAGTCAAA
1 TTCGCAACGCGAAT-TGTAAATCGCAACACAAAAGTCAAA
*
960 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAA-TTGTAAATCGCAACACAAAAGTCAAA
* * *
1000 TTTGCAACGCG-ATAGTCAAATTCGCAACACATAAGTCAAA
1 TTCGCAACGCGAATTGT-AAA-TCGCAACACAAAAGTCAAA
1040 TTCGCAACGCG
1 TTCGCAACGCG
1051 GAAGTCAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 74 0.90
41 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (39 bp):
TTCGCAACGCGAATTGTAAATCGCAACACAAAAGTCAAA
Found at i:986 original size:20 final size:20
Alignment explanation
Indices: 921--987 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
911 ATTTCCAATT
*
921 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
* * *
941 TCGTAACAC-AA-AAGTCAAA
1 TCGCAACGCGAATATGT-AAA
*
960 TTCGCAACGCGAATTTGTAAA
1 -TCGCAACGCGAATATGTAAA
981 TCGCAAC
1 TCGCAAC
988 ACAGAAGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 21 0.60
21 5 0.14
22 2 0.06
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1006 original size:20 final size:20
Alignment explanation
Indices: 945--1061 Score: 107
Period size: 20 Copynumber: 5.8 Consensus size: 20
935 TGTAAATCGT
*
945 AACACAAAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
*
965 AACGC-GAATTTGT-AAA-TCGC
1 AACACAGAA---GTCAAATTCGC
*
985 AACACAGAAGTCAAATTTGC
1 AACACAGAAGTCAAATTCGC
*
1005 AACGC-GATAGTCAAATTCGC
1 AACACAGA-AGTCAAATTCGC
*
1025 AACACATAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
* *
1045 AACGCGGAAGTCAAATT
1 AACACAGAAGTCAAATT
1062 TACAATGCGA
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.03
19 7 0.09
20 60 0.77
21 7 0.09
22 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGC
Found at i:1057 original size:40 final size:39
Alignment explanation
Indices: 876--1061 Score: 148
Period size: 40 Copynumber: 4.6 Consensus size: 39
866 AAATGACCAA
* * * * **
876 CAAATTTGTAACGCGAACTCCAAATTCGCAAC-CCAATTT
1 CAAATTCGCAACGCGAAGT-CAAATTCGCAACACAAAAGT
* *
915 CCAATTTCGCAACGCGAA-TCTGTAAA-TCGTAACACAAAAGT
1 -CAAATTCGCAACGCGAAGTC---AAATTCGCAACACAAAAGT
*
956 CAAATTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCGAA---GTCAAATTCGCAACACAAAAGT
* *
996 CAAATTTGCAACGCGATAGTCAAATTCGCAACACATAAGT
1 CAAATTCGCAACGCGA-AGTCAAATTCGCAACACAAAAGT
1036 CAAATTCGCAACGCGGAAGTCAAATT
1 CAAATTCGCAACGC-GAAGTCAAATT
1062 TACAATGCGA
Statistics
Matches: 121, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 103 0.85
41 10 0.08
44 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (39 bp):
CAAATTCGCAACGCGAAGTCAAATTCGCAACACAAAAGT
Found at i:1114 original size:20 final size:20
Alignment explanation
Indices: 1089--1128 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1079 TTTCGTAACA
*
1089 TGAATAGTAAAATCGCAACG
1 TGAATAGTAAAAGCGCAACG
1109 TGAATAGTAAAAGCGCAACG
1 TGAATAGTAAAAGCGCAACG
1129 AATCTATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (20 bp):
TGAATAGTAAAAGCGCAACG
Found at i:1516 original size:20 final size:21
Alignment explanation
Indices: 1478--1528 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1468 CAACGCGATT
*
1478 TTGCGATTTTCTAAATTCGTG
1 TTGCGATTTTCTAAATTCGCG
*
1499 TTGCGATTTT-TCAATTCGCG
1 TTGCGATTTTCTAAATTCGCG
1519 TTGCGATTTT
1 TTGCGATTTT
1529 ACTATTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (21 bp):
TTGCGATTTTCTAAATTCGCG
Found at i:1561 original size:40 final size:40
Alignment explanation
Indices: 1499--1609 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 40
1489 TAAATTCGTG
* * *
1499 TTGCGATTTTTCAATTCGCGTTGCGATTTTACTATTAACA
1 TTGCGATTTTACTATTCACGTTGCGATTTTACTATTAACA
* * *
1539 TTGTGATTTTACTATTCACGTTGCAATTTTACTATTCACA
1 TTGCGATTTTACTATTCACGTTGCGATTTTACTATTAACA
* * *
1579 TTGCAATTTTTACTATTCACGCTACGATTTT
1 TTGCGA-TTTTACTATTCACGTTGCGATTTT
1610 GGAAACTGAG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 38 0.64
41 21 0.36
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (40 bp):
TTGCGATTTTACTATTCACGTTGCGATTTTACTATTAACA
Found at i:1591 original size:21 final size:20
Alignment explanation
Indices: 1519--1598 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
1509 TCAATTCGCG
* *
1519 TTGCGATTTTACTATTAACA
1 TTGCAATTTTACTATTCACA
** *
1539 TTGTGATTTTACTATTCACG
1 TTGCAATTTTACTATTCACA
1559 TTGCAATTTTACTATTCACA
1 TTGCAATTTTACTATTCACA
1579 TTGCAATTTTTACTATTCAC
1 TTGCAA-TTTTACTATTCAC
1599 GCTACGATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 40 0.75
21 13 0.25
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (20 bp):
TTGCAATTTTACTATTCACA
Found at i:1609 original size:21 final size:20
Alignment explanation
Indices: 1498--1599 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 20
1488 CTAAATTCGT
* *
1498 GTTGCGATTTTT-CAATTCGC
1 GTTGC-ATTTTTACTATTCAC
*
1518 GTTGCGA-TTTTACTATTAAC
1 GTTGC-ATTTTTACTATTCAC
* *
1538 ATTGTGA-TTTTACTATTCAC
1 GTTG-CATTTTTACTATTCAC
*
1558 GTTGCAATTTTACTATTCAC
1 GTTGCATTTTTACTATTCAC
*
1578 ATTGCAATTTTTACTATTCAC
1 GTTGC-ATTTTTACTATTCAC
1599 G
1 G
1600 CTACGATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.07
20 48 0.72
21 14 0.21
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GTTGCATTTTTACTATTCAC
Found at i:1609 original size:41 final size:40
Alignment explanation
Indices: 1522--1609 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 40
1512 ATTCGCGTTG
** * *
1522 CGATTTTACTATTAACATTGTGATTTTACTATTCACGTTG
1 CGATTTTACTATTAACATTGCAATTTTACTATTCACGCTA
* *
1562 CAATTTTACTATTCACATTGCAATTTTTACTATTCACGCTA
1 CGATTTTACTATTAACATTGCAA-TTTTACTATTCACGCTA
1603 CGATTTT
1 CGATTTT
1610 GGAAACTGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (40 bp):
CGATTTTACTATTAACATTGCAATTTTACTATTCACGCTA
Found at i:1660 original size:19 final size:20
Alignment explanation
Indices: 1619--1664 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1609 TGGAAACTGA
* *
1619 GTTGCGAAATTGGAGTTCAC
1 GTTGCGAAATTCGAGATCAC
*
1639 GTTGC-AAATTCGAGATCGC
1 GTTGCGAAATTCGAGATCAC
1658 GTTGCGA
1 GTTGCGA
1665 TTTTATTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAATTCGAGATCAC
Found at i:2429 original size:57 final size:60
Alignment explanation
Indices: 2290--2433 Score: 197
Period size: 63 Copynumber: 2.4 Consensus size: 60
2280 AGAAAGTTAG
* *
2290 CTCATTTTGTCACTTTTAATAGTCTGGAGACTTAATAAGACAATGTCTTATAGTCGAAGTTAG
1 CTCATTTTGTCACTTTTAATAGTCTGGAGACTTAATAAAACAATG--TTATAGTCGAAG-TAA
2353 CTCATTTTGTCACTTTTAATAGTCTGGAGACTTAATAAAACAATG-TATAGTC-AGAG-AA
1 CTCATTTTGTCACTTTTAATAGTCTGGAGACTTAATAAAACAATGTTATAGTCGA-AGTAA
*
2411 CT-ATTTTGTAACTTTTAATAGTC
1 CTCATTTTGTCACTTTTAATAGTC
2434 GCGTGATTCA
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
57 20 0.26
58 3 0.04
59 1 0.01
60 9 0.12
63 44 0.57
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (60 bp):
CTCATTTTGTCACTTTTAATAGTCTGGAGACTTAATAAAACAATGTTATAGTCGAAGTAA
Found at i:2733 original size:2 final size:2
Alignment explanation
Indices: 2728--2763 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2718 TATAGAATTA
2728 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
2764 TTTAAGAAAA
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:7744 original size:3 final size:3
Alignment explanation
Indices: 7736--7766 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
7726 AAATGTCAAA
7736 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
7767 CCTGAAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9102 original size:53 final size:53
Alignment explanation
Indices: 9041--9158 Score: 202
Period size: 53 Copynumber: 2.2 Consensus size: 53
9031 CCTATGCATT
*
9041 AGGCAACTCATACTTAACCATTAAATCAAAACATCTAATGGATGTTCTTAATC
1 AGGCAACTCATACTTAACCAGTAAATCAAAACATCTAATGGATGTTCTTAATC
*
9094 AGGCAACTCATACTTAACCAGTAAATCAAAACATCTGATGGATGTTCTTAATC
1 AGGCAACTCATACTTAACCAGTAAATCAAAACATCTAATGGATGTTCTTAATC
*
9147 AAGCAA-TCATAC
1 AGGCAACTCATAC
9159 AGACAGCTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 6 0.10
53 56 0.90
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (53 bp):
AGGCAACTCATACTTAACCAGTAAATCAAAACATCTAATGGATGTTCTTAATC
Found at i:15803 original size:22 final size:22
Alignment explanation
Indices: 15777--15825 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
15767 CGGTACCTCT
*
15777 TGGGGGG-GAATATGTTCCCCC
1 TGGGGGGAAAATATGTTCCCCC
*
15798 TGGGGGGAAAATCTGTTCCCCC
1 TGGGGGGAAAATATGTTCCCCC
15820 TGGGGG
1 TGGGGG
15826 AATCTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.14, C:0.22, G:0.41, T:0.22
Consensus pattern (22 bp):
TGGGGGGAAAATATGTTCCCCC
Found at i:18645 original size:20 final size:20
Alignment explanation
Indices: 18585--18645 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
18575 CCGTTAGACA
*
18585 GGGGGCAATCAGTA-CCCCT
1 GGGGGGAATCAGTACCCCCT
* *
18604 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCAGTACCCCCT
*
18624 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCAGTACCCCCT
18644 GG
1 GG
18646 ACAATCTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 12 0.33
20 24 0.67
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGGGAATCAGTACCCCCT
Found at i:30021 original size:3 final size:3
Alignment explanation
Indices: 30008--30041 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
29998 CCTTCCTTTT
*
30008 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30042 AAGACATGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:34395 original size:19 final size:19
Alignment explanation
Indices: 34371--34407 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34361 CATCGAATGC
*
34371 AAGTAGTGTATCGATGCAT
1 AAGTAGTGCATCGATGCAT
34390 AAGTAGTGCATCGATGCA
1 AAGTAGTGCATCGATGCA
34408 CCCCCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (19 bp):
AAGTAGTGCATCGATGCAT
Found at i:36071 original size:23 final size:23
Alignment explanation
Indices: 36043--36128 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
36033 GACATTATAT
*
36043 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACGC
* * * *
36066 GCCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
36089 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
36112 GGCACTTCGATGCATTT
1 GGCACTACGGTGCATTT
36129 ATTCGAGCTG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:37314 original size:51 final size:51
Alignment explanation
Indices: 37254--37357 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
37244 GTAATAGATG
**
37254 AACCTTGGTAATCTTTGTCACAACTCATATTTAACCTTCCTAGGGAAACAT
1 AACCTTGGTAATCTTTGAAACAACTCATATTTAACCTTCCTAGGGAAACAT
* *
37305 AACCTTGGTAGTCTTTGAAACAACTCATATTTCACCTTCCTAGGGAAACAT
1 AACCTTGGTAATCTTTGAAACAACTCATATTTAACCTTCCTAGGGAAACAT
37356 AA
1 AA
37358 GATCATACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (51 bp):
AACCTTGGTAATCTTTGAAACAACTCATATTTAACCTTCCTAGGGAAACAT
Found at i:40368 original size:2 final size:2
Alignment explanation
Indices: 40361--40387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40351 GGACCTAAAG
40361 AT 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 A
40388 GCATTGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40549 original size:17 final size:17
Alignment explanation
Indices: 40515--40549 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40505 TTCGAACACC
*
40515 TAACCTTACTTAAGAGA
1 TAACCTTACTTAACAGA
*
40532 TAACCTTACTTGACAGA
1 TAACCTTACTTAACAGA
40549 T
1 T
40550 CTCACTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (17 bp):
TAACCTTACTTAACAGA
Found at i:41588 original size:22 final size:22
Alignment explanation
Indices: 41560--41614 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
41550 GAGGCAATAA
41560 ATGAATATGCAACAATATCTTC
1 ATGAATATGCAACAATATCTTC
*
41582 ATGAATATGCAACAATATCTTT
1 ATGAATATGCAACAATATCTTC
41604 ATGAATATGCA
1 ATGAATATGCA
41615 TTCTTACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
ATGAATATGCAACAATATCTTC
Found at i:42039 original size:29 final size:29
Alignment explanation
Indices: 41996--42105 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
41986 TTTTATATGT
41996 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
42024 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
42053 TCATATAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
42082 TCATGTAGCTCATGTTATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
42106 ATATCACATA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
28 7 0.09
29 63 0.84
30 5 0.07
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:42622 original size:64 final size:64
Alignment explanation
Indices: 42470--42626 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
42460 TAATGAAGGT
* * * * *
42470 ATGCATCGATTCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTGATTATTAATGGG
1 ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTGATTATTAAAGAG
* * * * * *
42534 ATGCATTGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATCTTTTTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGAT-GTTTGATTATTAAAG
42595 AG
63 AG
42597 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
42627 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 4 0.05
64 60 0.81
65 10 0.14
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTGATTATTAAAGAG
Found at i:50386 original size:18 final size:17
Alignment explanation
Indices: 50360--50395 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
50350 ATAGATTATT
50360 TATAAAAAATATTTAAAA
1 TATAAAAAAT-TTTAAAA
*
50378 TATATAAAATTTTAAAA
1 TATAAAAAATTTTAAAA
50395 T
1 T
50396 TTTAAGATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAAAAATTTTAAAA
Found at i:50843 original size:3 final size:3
Alignment explanation
Indices: 50782--50832 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
50772 AAGAAGAATT
50782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
50830 TTA
1 TTA
50833 ATTGTATTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52379 original size:31 final size:31
Alignment explanation
Indices: 52344--52411 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
52334 TTGCAATCCA
52344 GTCCCCCAACATTTAGTCCGTTTGCAATATG
1 GTCCCCCAACATTTAGTCCGTTTGCAATATG
52375 GTCCCCCAACATTTAGTCCGTTTGCAATATG
1 GTCCCCCAACATTTAGTCCGTTTGCAATATG
52406 GTCCCC
1 GTCCCC
52412 GGCGTAACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCGTTTGCAATATG
Found at i:57693 original size:41 final size:41
Alignment explanation
Indices: 57640--57736 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
57630 CGGTTTGTAA
57640 AAAAACCGGTTTTTTAAAAAAAAACCAGA-TTTTTT-CGGAT
1 AAAAACCGGTTTTTT-AAAAAAAACCAGATTTTTTTCCGGAT
* *
57680 AAAAATCCAGTTTTTT-AAAAAAACCGGATTTTTTTCCGGAT
1 AAAAA-CCGGTTTTTTAAAAAAAACCAGATTTTTTTCCGGAT
57721 AAAAACCGGTTTTTTA
1 AAAAACCGGTTTTTTA
57737 TCCGGTTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 11 0.22
40 20 0.40
41 19 0.38
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (41 bp):
AAAAACCGGTTTTTTAAAAAAAACCAGATTTTTTTCCGGAT
Found at i:57725 original size:23 final size:23
Alignment explanation
Indices: 57698--57741 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
57688 AGTTTTTTAA
57698 AAAAACCGGATTTTTT-TCCGGAT
1 AAAAACCGG-TTTTTTATCCGGAT
57721 AAAAACCGGTTTTTTATCCGG
1 AAAAACCGGTTTTTTATCCGG
57742 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (23 bp):
AAAAACCGGTTTTTTATCCGGAT
Found at i:57776 original size:27 final size:27
Alignment explanation
Indices: 57721--57776 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
57711 TTTTCCGGAT
* * ***
57721 AAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAACCAGTTTTTAATCCGGTAAAAA
57748 AAAAACCAGTTTTTAATCCGGTAAAAA
1 AAAAACCAGTTTTTAATCCGGTAAAAA
57775 AA
1 AA
57777 CCGGTCGTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (27 bp):
AAAAACCAGTTTTTAATCCGGTAAAAA
Found at i:58084 original size:10 final size:10
Alignment explanation
Indices: 58059--58127 Score: 59
Period size: 10 Copynumber: 6.5 Consensus size: 10
58049 ATGTAAAACT
*
58059 GTTGACTGACC
1 GTTGACCGA-C
*
58070 GTTGACCGGC
1 GTTGACCGAC
58080 GTTGACC-AC
1 GTTGACCGAC
58089 AGTTGACCTGAAC
1 -GTTGACC-G-AC
*
58102 TTTGACCGAC
1 GTTGACCGAC
58112 GTTGACCGAGC
1 GTTGACCGA-C
58123 GTTGA
1 GTTGA
58128 ACAACCGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.02
10 25 0.52
11 14 0.29
12 6 0.12
13 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.25
Consensus pattern (10 bp):
GTTGACCGAC
Found at i:58136 original size:22 final size:22
Alignment explanation
Indices: 58067--58137 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
58057 CTGTTGACTG
*
58067 ACCGTTGACCG-GCGTTG-ACC
1 ACCGTTGACCGAGCGTTGAACA
* * * * *
58087 ACAGTTGACCTGAACTTTGACCG
1 ACCGTTGACC-GAGCGTTGAACA
58110 A-CGTTGACCGAGCGTTGAACA
1 ACCGTTGACCGAGCGTTGAACA
58131 ACCGTTG
1 ACCGTTG
58138 TCTTTTTCCG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 9 0.24
21 10 0.27
22 16 0.43
23 2 0.05
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.23
Consensus pattern (22 bp):
ACCGTTGACCGAGCGTTGAACA
Found at i:60546 original size:24 final size:24
Alignment explanation
Indices: 60519--60649 Score: 131
Period size: 24 Copynumber: 5.5 Consensus size: 24
60509 ATATTTTATT
*
60519 TGATTTCTGA-CTTGAATTATGTTC
1 TGATTTCTGATC-TGAATTCTGTTC
* * * *
60543 TGA-TACATTACCTGAATTATGTTC
1 TGATTTC-TGATCTGAATTCTGTTC
* *
60567 TGATTTCTGATCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTC
* *
60591 TGATATCTGATCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTC
* *
60615 TGATATCTGATCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTC
60639 TGATTTCTGAT
1 TGATTTCTGAT
60650 ATCTCCGTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.02
24 87 0.95
25 3 0.03
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTC
Found at i:60580 original size:12 final size:12
Alignment explanation
Indices: 60565--60649 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
60555 TGAATTATGT
60565 TCTGATTTCTGA
1 TCTGATTTCTGA
*
60577 TCTGGA-TTCTGT
1 TCT-GATTTCTGA
* *
60589 TATGATATCTGA
1 TCTGATTTCTGA
* *
60601 TCTGAATTCTGT
1 TCTGATTTCTGA
* *
60613 TTTGATATCTGA
1 TCTGATTTCTGA
* *
60625 TCTGAATTCTGT
1 TCTGATTTCTGA
*
60637 TTTGATTTCTGA
1 TCTGATTTCTGA
60649 T
1 T
60650 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 19, Indels: 4
0.69 0.25 0.05
Matches are distributed among these distances:
11 2 0.04
12 48 0.92
13 2 0.04
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGA
Found at i:65258 original size:12 final size:12
Alignment explanation
Indices: 65243--65302 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
65233 GATACATTAC
65243 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
65255 CTGATTTCTGAT
1 CTGAATTCTGTT
*
65267 CTGGATTCTGTT
1 CTGAATTCTGTT
* *
65279 ATG-ATATCTGAT
1 CTGAAT-TCTGTT
65291 CTGAATTCTGTT
1 CTGAATTCTGTT
65303 TTGATTTATG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:65274 original size:24 final size:24
Alignment explanation
Indices: 65243--65314 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
65233 GATACATTAC
*
65243 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
65267 CTGGATTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
65291 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTATGATTTCTGAT
65315 ATCTCCGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:65275 original size:48 final size:49
Alignment explanation
Indices: 65210--65314 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 49
65200 ATTTTATCTA
* *
65210 ATTTCTGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGTTCTG
1 ATTTCTGATCTTGAATTCTGTTATGATATC-TGACCTGAATTCTGTTCTG
* * *
65258 ATTTCTGATC-TGGATTCTGTTATGATATCTGATCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGTTATGATATCTGACCTGAATTCTGTTCTG
*
65306 ATTTATGAT
1 ATTTCTGAT
65315 ATCTCCGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTCTGTTATGATATCTGACCTGAATTCTGTTCTG
Found at i:72347 original size:42 final size:41
Alignment explanation
Indices: 72287--72402 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 41
72277 TCCGAAATTT
*
72287 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATATTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATA-TTTTC
* *
72329 CGTGTTTGTTGCACGTAATTCGTTTTTCGGAAAATATTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTC
*
72370 CAGTGTTTGTTTCACATAATTCGTTTTCCGGAA
1 C-GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
72403 CGTAATTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 6 0.09
42 61 0.91
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTC
Found at i:72638 original size:22 final size:23
Alignment explanation
Indices: 72591--72651 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
72581 TAATTATTAA
* *
72591 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
72612 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
72635 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
72652 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:72762 original size:28 final size:27
Alignment explanation
Indices: 72607--72763 Score: 80
Period size: 28 Copynumber: 5.7 Consensus size: 27
72597 TAAAATATAT
72607 TTATTAATATTT-ATAATAAT-ATAATA
1 TTATT-ATATTTAATAATAATAATAATA
* *
72633 TTA-TATTTTTAATATTATATAA-AATAA
1 TTATTATATTTAATAATA-ATAATAAT-A
* *
72660 TCAATTATATTATAATAAT-ATAA-GATA
1 T-TATTATATT-TAATAATAATAATAATA
* *
72687 TTATTTTTTATTTTAATAATATATAATAAAAAA
1 TTA--TTATA-TTTAATAATA-ATAAT--AATA
72720 TT-TTATATATT--TAATAATGAATAATA
1 TTATTATAT-TTAATAATAAT-AATAATA
72746 TTATTATATTTAATAATA
1 TTATTATATTTAATAATA
72764 TTTTAATAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 38
0.66 0.08 0.26
Matches are distributed among these distances:
24 5 0.05
25 6 0.06
26 16 0.16
27 13 0.13
28 31 0.31
29 8 0.08
30 16 0.16
33 4 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TTATTATATTTAATAATAATAATAATA
Done.